LiteFold/DisProt huggingface dataset:
Protein: DP03944 (UniProt P19525)
Region: residues 441	to 451
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Thus, it is noteworthy that helix αG occupies that same position in the absence of substrate. As is typical of structures of unphosphorylated protein kinases, portions of the activation loop are disordered (A: 441–450, B:440–450), but in chain C a shorter region is disordered (447–449). 
Residues 256–257, 441–450, and 335–355 from chain A, 255, 334–355, and 439–451 from chain B, and 334–356, 441–444, and 449 from chain C were inserted and Prime version 1 (Schrödinger, LLC)44 was used to generate a configuration of the missing loops.
Cross-references: PDB:6D3K
PDB:6D3L
Protein: DP03944 (UniProt P19525)
Region: residues 542	to 551
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:6D3L
Protein: DP03944 (UniProt P19525)
Region: residues 170	to 251
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 81-amino-acid linker (residues 170-251) is acidic (estimated pI of 4.3) and hydrophilic, with 24 serines and threonines. Both the kinase and the dsRBD domains are basic and structured. Our NMR data strongly suggest that the linker region is mainly unstructured in PKR.
Protein: DP03944 (UniProt P19525)
Region: residues 170	to 251
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 81-amino-acid linker (residues 170-251) is acidic (estimated pI of 4.3) and hydrophilic, with 24 serines and threonines. Both the kinase and the dsRBD domains are basic and structured. Our NMR data strongly suggest that the linker region is mainly unstructured in PKR.
Protein: DP03944 (UniProt P19525)
Region: residues 80	to 100
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The linker between the two dsRBMs was found to be long and highly flexible, as shown by the random chemical shift nature, small and negative heteronuclear amide 1H{15N} nuclear Overhauser effects (NOEs) in this region (Figure 3). In fact, no long-range NOEs and few medium-range NOEs were identified in this region due to its high flexibility.
Cross-references: PDB:1QU6
Protein: DP03944 (UniProt P19525)
Region: residues 80	to 100
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The linker between the two dsRBMs was found to be long and highly flexible, as shown by the random chemical shift nature, small and negative heteronuclear amide 1H{15N} nuclear Overhauser effects (NOEs) in this region (Figure 3). In fact, no long-range NOEs and few medium-range NOEs were identified in this region due to its high flexibility.
The structure of dsRBD exhibits a dumb-bell shape, with the two dsRBMs flanking a 22 residue linker region (Figure 2A).
Cross-references: PDB:1QU6
Protein: DP03944 (UniProt P19525)
Region: residues 444	to 448
Annotation: phosphorylation display site (Disorder function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Finally, mutations at either or both of two key phosphorylation sites in the activation loop (T446A and T451A) result in attenuation of phosphorylation by PKRP.
Protein: DP03944 (UniProt P19525)
Region: residues 446	to 451
Annotation: phosphorylation display site (Disorder function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Finally, mutations at either or both of two key phosphorylation sites in the activation loop (T446A and T451A) result in attenuation of phosphorylation by PKRP.
Protein: DP03945 (UniProt Q16620)
Region: residues 385	to 426
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:5MO9
Protein: DP03946 (UniProt Q9Y6K1)
Region: residues 831	to 846
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues on the missing loop (residues 831–846) were mutated for the in vitro DNA methyltransferase activity assay.
Cross-references: PDB:4U7T
PDB:4U7P
Protein: DP03946 (UniProt Q9Y6K1)
Region: residues 455	to 473
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:4U7P
Protein: DP03946 (UniProt Q9Y6K1)
Region: residues 831	to 846
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
DNMT3A binding to DNA is mainly mediated by a loop from the target recognition domain (TRD) (residues R831-F848), the catalytic loop (residues G707-K721) and the homodimeric interface of DNMT3A, which together create a continuous DNA-binding surface (Fig. 1d, 2a).  Accordingly, these segments exhibit the most prominent structural changes upon DNA binding – the TRD loop lacked electron density in the DNA-free structure of DNMT3A–DNMT3L11, 12, but became well defined upon DNA binding and penetrated into the DNA major groove for intermolecular contacts (Fig. 2a–c); additionally, the TRD loop is stabilized through hydrogen-bonding interactions with R882, the DNMT3A mutational hotspot among leukemias9, 10, and Q886 from an adjacent helix (Fig. 2c).
The authors are referring to the 831–846 region described in the cited publication (PMID 25383530) as disordered.
Cross-references: PDB:6F57
PDB:5YX2
DisProt:DP03946r001
Protein: DP03946 (UniProt Q9Y6K1)
Region: residues 831	to 846
Annotation: DNA binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
DNMT3A binding to DNA is mainly mediated by a loop from the target recognition domain (TRD) (residues R831-F848), the catalytic loop (residues G707-K721) and the homodimeric interface of DNMT3A, which together create a continuous DNA-binding surface (Fig. 1d, 2a). Accordingly, these segments exhibit the most prominent structural changes upon DNA binding – the TRD loop lacked electron density in the DNA-free structure of DNMT3A–DNMT3L11, 12, but became well defined upon DNA binding and penetrated into the DNA major groove for intermolecular contacts (Fig. 2a–c); additionally, the TRD loop is stabilized through hydrogen-bonding interactions with R882, the DNMT3A mutational hotspot among leukemias9, 10, and Q886 from an adjacent helix (Fig. 2c).
The authors are referring to the 831–846 region described in the cited publication (PMID 25383530) as disordered.
For the covalent DNMT3A–DNMT3L–DNA complex (PDB 6F57), a 11-mer single-stranded DNA that was in-house synthesized to contain 2′-deoxy-Zebularine (5′- CATGdZGCTCTC -3′, dZ = 2′-deoxy-Zebularine) annealed to a 10-mer single-stranded DNA (5′- AGAGCGCATG -3′). For the Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites (PDB 5YX2) a 25-mer Zebularine-containing DNA (5′- GCATGZGTTCTAATTAGAACGCATG -3′, Z = Zebularine) was self-annealed.
Formation of the DNMT3A–DNA complex is also supported by various protein–DNA interactions flanking CpG, which involve electrostatic and/or hydrogen-bonding interactions of the TRD residues (R831, T832, T835, N838 and K841), catalytic loop residues (N711, S714 and I715) and DNMT3A–DNMT3A homodimeric interface residues (S881, R882, L883 and R887) with various DNA backbone or base sites (Fig. 2a and Extended Data Fig. 3a–f).
Cross-references: PDB:6F57
PDB:5YX2
Protein: DP03946 (UniProt Q9Y6K1)
Region: residues 831	to 846
Annotation: unmethylated CpG binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
DNMT3A binding to DNA is mainly mediated by a loop from the target recognition domain (TRD) (residues R831-F848), the catalytic loop (residues G707-K721) and the homodimeric interface of DNMT3A, which together create a continuous DNA-binding surface (Fig. 1d, 2a).  Accordingly, these segments exhibit the most prominent structural changes upon DNA binding – the TRD loop lacked electron density in the DNA-free structure of DNMT3A–DNMT3L11, 12, but became well defined upon DNA binding and penetrated into the DNA major groove for intermolecular contacts (Fig. 2a–c); additionally, the TRD loop is stabilized through hydrogen-bonding interactions with R882, the DNMT3A mutational hotspot among leukemias9, 10, and Q886 from an adjacent helix (Fig. 2c).
Recognition of CpG dinucleotides by DNMT3A is mediated by both catalytic and TRD loops. In particular, guanine of the target strand, G6 (G19′), is specified by a hydrogen bond between its O6 atom and the Nε atom of R836 from the TRD loop, as well as water-mediated hydrogen bonds between its N7 atom and the Nε and Oγ atoms of R836 and T834, respectively (Fig. 3a).
For the covalent DNMT3A–DNMT3L–DNA complex (PDB 6F57), a 11-mer single-stranded DNA that was in-house synthesized to contain 2′-deoxy-Zebularine (5′- CATGdZGCTCTC -3′, dZ = 2′-deoxy-Zebularine) annealed to a 10-mer single-stranded DNA (5′- AGAGCGCATG -3′). For the Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites (PDB 5YX2) a 25-mer Zebularine-containing DNA (5′- GCATGZGTTCTAATTAGAACGCATG -3′, Z = Zebularine) was self-annealed. Zebularine is a cytidine analog that acts as a methylation inhibitor.
Cross-references: PDB:6F57
PDB:5YX2
Protein: DP03947 (UniProt P0A8J8)
Region: residues 404	to 421
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited protease digestion shows that the highly basic C-terminal 2 kDa fragment of the helicase is readily cleaved by trypsin (residues 403–420, confirmed by mass spectrometry analysis) and that the core of the protein is comparatively more resistant to further digestion (results not shown).
Authors are referring to the 404-421 region since they are not considering the first Met residue.
Protein: DP03948 (UniProt Q8WQM8)
Region: residues 1	to 28
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
Major differences arise due to artemin having a 28 residue long disordered N-terminus region as well as an additional helix (F) and a second long disordered loop (L′) (Figure 2A, Supplementary Figure S3).
Cross-references: PDB:7RVB
EMDB:24706
Protein: DP03948 (UniProt Q8WQM8)
Region: residues 194	to 214
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
Major differences arise due to artemin having a 28 residue long disordered N-terminus region as well as an additional helix (F) and a second long disordered loop (L′) (Figure 2A, Supplementary Figure S3).
Cross-references: PDB:7RVB
EMDB:24706
Protein: DP03949 (UniProt O15294-3)
Region: residues 747	to 760
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:7NTF
Protein: DP03949 (UniProt O15294-3)
Region: residues 1	to 78
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We note that without crystal formation, TPR units N-terminal of the dimer interface exhibit considerably conformational heterogeneity and could only be partly resolved by particle subtraction, hinting that flexibility in this section may play a role in how OGT selects larger substrates.
Early maps generated during data processing provided density into which only the catalytic domain appended to TPR units 6-13.5 could be modelled, TPR units N-terminal of the dimer interface (TPRs 1–5) exhibited high heterogeneity, suggestive of flexibility in the TPR units of this region.
Cross-references: PDB:7NTF
Protein: DP03950 (UniProt Q02020)
Region: residues 1	to 61
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The amino-terminal segments of the α and β chains, including fibrinopeptides A and B, are not visible in electron density maps, however, and must be highly disordered.
Electron density maps barely reveal the outlines of the disordered carboxyl regions of the α chains (Figure 2), and the amino-terminal segments of the α and β chains, including fibrinopeptides A and B, could not be resolved. The reasonable R-factors found after refinement (Table 1) indicate that these parts of the molecule do not contribute significantly to the diffraction and must be highly disordered. That the missing portions had not been lost to degradation during incubations leading to crystallization was ascertained by SDS gels and amino-terminal sequencing.
Cross-references: PDB:1M1J
Protein: DP03951 (UniProt O93568)
Region: residues 420	to 435
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As such, almost 30% of the residues are missing (Table 1), mostly from the αC domain (272 residues), but also the amino-terminal segments of the three chains (96 residues all told) and the γ chain carboxyl-terminal segment (16 residues).
Cross-references: PDB:1M1J
Protein: DP03951 (UniProt O93568)
Region: residues 30	to 111
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region has high B-factor values, indicating this region is highly flexible and presumed as disordered. 
Cross-references: PDB:1M1J
Protein: DP03952 (UniProt Q13224)
Region: residues 1	to 33
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:7EU8
EMDB:EMD-31309
Protein: DP03952 (UniProt Q13224)
Region: residues 201	to 212
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:7EU8
EMDB:EMD-31309
Protein: DP03952 (UniProt Q13224)
Region: residues 393	to 402
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:7EU8
EMDB:EMD-31309
Protein: DP03952 (UniProt Q13224)
Region: residues 580	to 599
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:7EU8
EMDB:EMD-31309
Protein: DP03953 (UniProt P43034)
Region: residues 298	to 307
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:8DYU
PDB:8DYV
EMDB:EMD-27783
EMDB:EMD-27782
Protein: DP03955 (UniProt P33897)
Region: residues 2	to 63
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.
The N-terminal residues 1–66, a loop region (residues 357–365), and the C-terminal residues 708–745 were not resolved. Additionally, the hinge region (residues 437–462) between TMD and NBD was invisible in the electron density probably due to flexibility.
Cross-references: PDB:7SHM
PDB:7SHN
EMDB:EMD-25130
EMDB:EMD-25131
Protein: DP03955 (UniProt P33897)
Region: residues 437	to 461
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal residues 1–66, a loop region (residues 357–365), and the C-terminal residues 708–745 were not resolved. Additionally, the hinge region (residues 437–462) between TMD and NBD was invisible in the electron density probably due to flexibility.
Cross-references: PDB:7SHM
PDB:7SHN
EMDB:EMD-25130
EMDB:EMD-25131
Protein: DP03955 (UniProt P33897)
Region: residues 353	to 375
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.
The N-terminal residues 1–66, a loop region (residues 357–365), and the C-terminal residues 708–745 were not resolved. Additionally, the hinge region (residues 437–462) between TMD and NBD was invisible in the electron density probably due to flexibility.
Cross-references: PDB:7SHM
EMDB:EMD-25130
Protein: DP03955 (UniProt P33897)
Region: residues 684	to 745
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.
The N-terminal residues 1–66, a loop region (residues 357–365), and the C-terminal residues 708–745 were not resolved. Additionally, the hinge region (residues 437–462) between TMD and NBD was invisible in the electron density probably due to flexibility.
Cross-references: PDB:7SHM
EMDB:EMD-25130
Protein: DP03956 (UniProt O14678)
Region: residues 2	to 12
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.
The final model composed of residues Arg13-Lys604, except for a 27-aa linker region (residues Lys357-Ala383), was refined against the EM density to an excellent geometry and statistics (Supplementary information, Fig. S2f and Table S1).
Cross-references: PDB:6JBJ
EMDB:EMD-9791
Protein: DP03956 (UniProt O14678)
Region: residues 357	to 383
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model composed of residues Arg13-Lys604, except for a 27-aa linker region (residues Lys357-Ala383), was refined against the EM density to an excellent geometry and statistics (Supplementary information, Fig. S2f and Table S1).
Cross-references: PDB:6JBJ
EMDB:EMD-9791
Protein: DP03956 (UniProt O14678)
Region: residues 357	to 383
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model composed of residues Arg13-Lys604, except for a 27-aa linker region (residues Lys357-Ala383), was refined against the EM density to an excellent geometry and statistics (Supplementary information, Fig. S2f and Table S1).
Cross-references: PDB:6JBJ
EMDB:EMD-9791
Protein: DP03957 (UniProt P60709)
Region: residues 33	to 78
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, electron microscopy demonstrates nucleosome-bound human BAF complex where multiple proteins and DNA molecules are interacting.
Cross-references: PDB:6LTJ
EMDB:EMD-0974
Protein: DP03958 (UniProt O96019)
Region: residues 45	to 67
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. Furthermore, the structure demonstrates a nucleosome-bound human BAF complex where multiple proteins and DNA molecules are interacting.
Cross-references: PDB:6LTJ
EMDB:EMD-0974
Protein: DP03958 (UniProt O96019)
Region: residues 216	to 245
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. Furthermore, the structure demonstrates a nucleosome-bound human BAF complex where multiple proteins and DNA molecules are interacting.
Cross-references: PDB:6LTJ
EMDB:EMD-0974
Protein: DP03958 (UniProt O96019)
Region: residues 312	to 322
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. Furthermore, the structure demonstrates a nucleosome-bound human BAF complex where multiple proteins and DNA molecules are interacting.
Cross-references: PDB:6LTJ
EMDB:EMD-0974
Protein: DP03958 (UniProt O96019)
Region: residues 1	to 11
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 45	to 67
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