LiteFold/DisProt huggingface dataset:
Protein: DP03958 (UniProt O96019)
Region: residues 216	to 245
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered. Furthermore, the electron microscopy structure is associated with the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome.
Cross-references: PDB:7VDV
Protein: DP03958 (UniProt O96019)
Region: residues 312	to 322
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered. Furthermore, the electron microscopy structure is associated with the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome.
Cross-references: PDB:7VDV
Protein: DP03958 (UniProt O96019)
Region: residues 418	to 429
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered. Furthermore, the electron microscopy structure is associated with the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome.
Cross-references: PDB:7VDV
Protein: DP03959 (UniProt Q9Y653)
Region: residues 549	to 559
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:7SF8
Protein: DP03959 (UniProt Q9Y653)
Region: residues 664	to 693
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:7SF8
Protein: DP03960 (UniProt P55263)
Region: residues 348	to 362
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region when bound to an inhibitor, indicating it is disordered.
Cross-references: PDB:2I6B
Protein: DP03961 (UniProt Q9NX46)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:7L9F
PDB:7L9H
PDB:7L9I
Protein: DP03961 (UniProt Q9NX46)
Region: residues 60	to 69
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:7L9F
PDB:7L9H
Protein: DP03962 (UniProt P30566)
Region: residues 283	to 294
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Similar to the ADSL-R303C and ADSL-SAMP, electron density for residues 283–293 (β3-α10 loop) was not observed.
Cross-references: PDB:4FFX
Protein: DP03962 (UniProt P30566)
Region: residues 475	to 484
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Electron density was observed for the majority of all 5–476 ADSL residues in all monomers, with residues 5–112 forming domain 1, residues 113–364 as domain 2, and 364–476 as domain 3.
Cross-references: PDB:4FFX
Protein: DP03963 (UniProt O95831)
Region: residues 78	to 125
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
To test whether the crystallographic monomer and dimer accurately reveal AIF architecture in solution or reflect crystal packing, we collected SAXS data on soluble constructs with increasing NADH concentrations: AIF78 (residues 78–613, the intact mitochondrial protein save the 24-residue transmembrane insert, residues 54–77), and AIF121 (residues 121–613, excluding the disordered N-terminal linker to the membrane) (Figure 1A, S2).
Cross-references: PDB:5KVI
PDB:5KVH
Protein: DP03963 (UniProt O95831)
Region: residues 511	to 559
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
AIF78 W196A forms the dimeric interface seen in the wild-type AIF-CTC crystal structure (PDB: 4BUR) and is missing density for the displaced C-loop insert (Figure 3A).
Point mutations along the C-loop backbone promoted partial C-loop exposure without ligand and more efficient protein dimerization at lower NADH levels relative to wild-type protein (Figures 2C–D, top).
Cross-references: PDB:5KVH
Protein: DP03963 (UniProt O95831)
Region: residues 545	to 556
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:5KVI
Protein: DP03963 (UniProt O95831)
Region: residues 78	to 121
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Corresponding values derived from AIF78 (Rg 28.9 Å and Vp 101,858 Å3) are elevated relative to the crystal structure, consistent with added scattering volume from the 43-residue N-terminus.
Protein: DP03963 (UniProt O95831)
Region: residues 546	to 558
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues following these two α-helices are organized in a loop (533–545) and, high flexibility beyond position 546 makes the rest of the region not visible (546–558).
Cross-references: PDB:4BV6
Protein: DP03963 (UniProt O95831)
Region: residues 517	to 550
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The four chains of the asymmetric unit present a similar overall fold: r.m.s.d. of 0.28 Å (412 Cα, chain B), 0.24 Å (373 Cα, C), and 0.30 Å (384 Cα, D) regarding chain A. The final atomic model contains residues 128–516 and 551–611 in chain A, 125–516 and 553–610 in B, 127–517 and 558–612 in C, and 128–509 and 559–611 in D, and electron density was clear to position one FAD and two NAD(H) molecules per hAIFΔ1–102 protomer with 100% occupancy (Figure 2).
Cross-references: PDB:4BUR
Protein: DP03963 (UniProt O95831)
Region: residues 103	to 127
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The four chains of the asymmetric unit present a similar overall fold: r.m.s.d. of 0.28 Å (412 Cα, chain B), 0.24 Å (373 Cα, C), and 0.30 Å (384 Cα, D) regarding chain A. The final atomic model contains residues 128–516 and 551–611 in chain A, 125–516 and 553–610 in B, 127–517 and 558–612 in C, and 128–509 and 559–611 in D, and electron density was clear to position one FAD and two NAD(H) molecules per hAIFΔ1–102 protomer with 100% occupancy (Figure 2).
Cross-references: PDB:4BUR
Protein: DP03963 (UniProt O95831)
Region: residues 517	to 545
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Upon coenzyme binding and/or reduction R201 results are displaced by forming a H-bond with the main chains of Y204 and S202, thus, contributing to the unfolding of the short helices, allowing NAD(H)B stabilization and releasing the orientation of the 190–202 β-hairpin to the solvent. Overall, these results uncover that at a molecular level, the oxido-reduction and/or coenzyme-bound status of hAIF modulates the conformation of its C-terminal proapoptotic domain.
Cross-references: PDB:4BV6
PDB:4BUR
Protein: DP03963 (UniProt O95831)
Region: residues 517	to 545
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In hAIFox the 517–533 region is stabilized by direct interaction with the 190–202 β-hairpin, particularly by a H-bond and a salt-bridge between the side-chain of R201 and those of T526 and E531, respectively.
Cross-references: PDB:4BV6
Protein: DP03964 (UniProt P47895)
Region: residues 1	to 26
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:6TRY
Protein: DP03964 (UniProt P47895)
Region: residues 1	to 19
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:7QK8
PDB:7QK7
Protein: DP03965 (UniProt P30038)
Region: residues 512	to 537
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The active site of S352L, however, is highly perturbed. In particular, the catalytic loop adopts a non-native conformation (Fig. 7a).
Cross-references: PDB:3V9I
Protein: DP03965 (UniProt P30038)
Region: residues 552	to 563
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As in the Put2p structure, electron density for the aldehyde anchor peptide of monoclinic HsP5CDH (residues 514–535) is very weak (Figure3C). Electron density for these residues is essentially absent in chains A and D, and the entire loop was omitted. In the other two chains in the asymmetric unit, the binding of Mg2+ from the crystallization buffer stabilizes residues 522–535 in a non-native conformation, but the other residues of the loop remain disordered. Thus, the disordered active site is not limited to Put2p.
Cross-references: PDB:4OE5
Protein: DP03966 (UniProt P49419)
Region: residues 487	to 509
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The tetragonal structures, which were determined in the absence of bound AA, suggest a more severe conformational variation of the active site. In these structures, electron density for the 12 C-terminal residues (500–511) is absent in both chains in the asymmetric unit. Similarly, electron density for the long interdomain linker (residues 459–481) is missing.
The authors are referring to the 528-539 and 487-509 regions of the UniProt sequence.
Cross-references: PDB:4ZVY
PDB:4ZVX
Protein: DP03966 (UniProt P49419)
Region: residues 528	to 539
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The tetragonal structures, which were determined in the absence of bound AA, suggest a more severe conformational variation of the active site. In these structures, electron density for the 12 C-terminal residues (500–511) is absent in both chains in the asymmetric unit. Similarly, electron density for the long interdomain linker (residues 459–481) is missing.
The authors are referring to the 528-539 and 487-509 regions of the UniProt sequence.
Thus, the P4212 lattice seems to be compatible with the open (and closed) conformation of the C-terminus. The absence of electron density implies that the C-terminus adopts multiple conformations in the P4212 crystal. Apparently, the solvent channel is large enough to accommodate multiple, diverse conformations of the C-terminus.
Cross-references: PDB:4ZVY
PDB:4ZVX
Protein: DP03966 (UniProt P49419)
Region: residues 487	to 509
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The tetragonal structures, which were determined in the absence of bound AA, suggest a more severe conformational variation of the active site. In these structures, electron density for the 12 C-terminal residues (500–511) is absent in both chains in the asymmetric unit. Similarly, electron density for the long interdomain linker (residues 459–481) is missing.
The authors are referring to the 528-539 and 487-509 regions of the UniProt sequence.
Cross-references: PDB:4ZVX
PDB:4ZVY
Protein: DP03967 (UniProt Q96BT7)
Region: residues 159	to 173
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 156–174 and 181–192 in the AlkB domain (dotted green lines), which are topologically equivalent to the segments forming the nucleotide-binding lid in E. coli AlkB, are disordered in ABH8.
Cross-references: PDB:3THP
PDB:3THT
Protein: DP03967 (UniProt Q96BT7)
Region: residues 182	to 191
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 156–174 and 181–192 in the AlkB domain (dotted green lines), which are topologically equivalent to the segments forming the nucleotide-binding lid in E. coli AlkB, are disordered in ABH8.
Cross-references: PDB:3THP
Protein: DP03968 (UniProt Q01433)
Region: residues 229	to 248
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:8HUB
Protein: DP03968 (UniProt Q01433)
Region: residues 390	to 441
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structural information revealed that compound 8 is accommodated in a new pocket upon the conformational change in the AMPD2-AMP co-structure, while the flexible loop was not visible.
Cross-references: PDB:8HUB
Protein: DP03968 (UniProt Q01433)
Region: residues 228	to 248
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:8HU6
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 33	to 70
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 134	to 145
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 193	to 205
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 277	to 403
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 513	to 580
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 671	to 703
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 732	to 756
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 815	to 838
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 883	to 923
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 987	to 1012
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9T
PDB:5L9U
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 1334	to 1346
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9T
PDB:5L9U
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 1438	to 1451
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9T
PDB:5L9U
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 1705	to 1746
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9T
PDB:5L9U
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 1756	to 1769
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9T
PDB:5L9U
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 1828	to 1838
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9T
PDB:5L9U
EMDB:3432
EMDB:3433
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 1896	to 1907
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433