4z8l

Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex

Method: X-RAY DIFFRACTION D_max: 107.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein VPRBP

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1057–1396	Fragment：UNP residues 1057-1396	Vpx protein × 1 （Q7ZB17） SAM domain and HD domain-containing protein × 1 （H6WEA4） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2	Resolution 2.60 Å R-free 0.228
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 1057–1396	Fragment：UNP residues 1057-1396	Vpx protein × 1 （Q7ZB17） SAM domain and HD domain-containing protein × 1 （H6WEA4） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2	Resolution 2.60 Å R-free 0.228

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4Z8L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WA0 Crystal structure of merlin complexed with DCAF1/VprBP Deposited 2013-04-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1417–1506（90 aa） Fragment：UNP residues 1417-1506	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；0.2M ammonium fluoride, 23% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.31 Å R-free 0.264
3WA0 Crystal structure of merlin complexed with DCAF1/VprBP Deposited 2013-04-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1417–1506（90 aa） Fragment：UNP residues 1417-1506	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；0.2M ammonium fluoride, 23% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.31 Å R-free 0.264
4CC9 Crystal structure of human SAMHD1 (amino acid residues 582-626) bound to Vpx isolated from sooty mangabey and human DCAF1 (amino acid residues 1058-1396) Deposited 2013-10-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1058–1396（339 aa） Fragment：RESIDUES 1058-1396	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 15% PEG 400	Resolution 2.47 Å R-free 0.216
4P7I Crystal structure of the Merlin FERM/DCAF1 complex Deposited 2014-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 998–1058（61 aa） Fragment：UNP residues 998-1058	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% Isopropanol and 5% PEG8000	Resolution 2.60 Å R-free 0.256
4P7I Crystal structure of the Merlin FERM/DCAF1 complex Deposited 2014-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 998–1058（61 aa） Fragment：UNP residues 998-1058	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% Isopropanol and 5% PEG8000	Resolution 2.60 Å R-free 0.256
4PXW Crystal structure of human DCAF1 WD40 repeats (Q1250L) Deposited 2014-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1039–1401（363 aa）	Mutation：Q1250L	UNX UNKNOWN LIGAND × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M sodium hepes, 0.2 M lithium sulfate, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 291K	Resolution 1.72 Å R-free 0.219
4PXW Crystal structure of human DCAF1 WD40 repeats (Q1250L) Deposited 2014-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1039–1401（363 aa）	Mutation：Q1250L	UNX UNKNOWN LIGAND × 23	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M sodium hepes, 0.2 M lithium sulfate, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 291K	Resolution 1.72 Å R-free 0.219
5AJA Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) bound to Vpx isolated from mandrill and human DCAF1 (amino acid residues 1058-1396) Deposited 2015-02-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1058–1396（339 aa） Fragment：WD40-REPEAT DOMAIN, RESIDUES 1058-1396	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.16 M TRISODIUM CITRATE-HCL PH 5.2, 4% PEG 6000	Resolution 2.65 Å R-free 0.227
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1045–1396（352 aa） Fragment：UNP residues 1045-1396	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000	Resolution 3.49 Å R-free 0.206
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1045–1396（352 aa） Fragment：UNP residues 1045-1396	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000	Resolution 3.49 Å R-free 0.206
6N45 Crystal structure of the cryptic polo box domain of human activated Plk4 variant 1 Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1475–1507（33 aa） Chain B 1475–1507（33 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；4.3M Ammonium Acetate 0.1M BisTris propane pH 8.0	Resolution 2.64 Å R-free 0.314
6ZUE Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1046–1396（351 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；100 mM Tri-Na citrate pH 5.5 18% PEG 1000	Resolution 3.09 Å R-free 0.279
6ZX9 Crystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1046–1396（351 aa）	Not recorded	GOL GLYCEROL × 8 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2.	Resolution 2.52 Å R-free 0.260
7OKQ Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex Deposited 2021-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: Hexadecameric	Chain B 2–1507（1506 aa） Chain F 2–1507（1506 aa） Chain J 2–1507（1506 aa） Chain N 2–1507（1506 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.40 Å
7SSE Crystal structure of the WDR domain of human DCAF1 in complex with CYCA-117-70 Deposited 2021-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1077–1390（314 aa） Chain B 1077–1390（314 aa）	Mutation：F1077A, R1079A Mutation：F1077A, R1079A	B1I N-[(3R)-1-(3-fluorophenyl)piperidin-3-yl]-6-(morpholin-4-yl)pyrimidin-4-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；30% PEG3350 ,0.1M Ammonium Sulphate, 0.1M Bis-Tris pH5.5	Resolution 1.62 Å R-free 0.234
7UFV Crystal structure of the WDR domain of human DCAF1 in complex with OICR-6766 Deposited 2022-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1077–1390（314 aa）	Mutation：F1077A, R1079A	N6O (3P)-N-[(1S)-3-amino-1-(3-chlorophenyl)-3-oxopropyl]-3-(2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；20% PEG3350, 0.2M Potassium Fluoride	Resolution 1.90 Å R-free 0.254
7UFV Crystal structure of the WDR domain of human DCAF1 in complex with OICR-6766 Deposited 2022-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1077–1390（314 aa）	Mutation：F1077A, R1079A	N6O (3P)-N-[(1S)-3-amino-1-(3-chlorophenyl)-3-oxopropyl]-3-(2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 UNX UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；20% PEG3350, 0.2M Potassium Fluoride	Resolution 1.90 Å R-free 0.254
7V7B CryoEM structure of DDB1-VprBP complex in ARM-up conformation Deposited 2021-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1507（1507 aa） Chain C 1–1507（1507 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7V7C CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex Deposited 2021-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1507（1507 aa） Chain E 1–1507（1507 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8F8E Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound Deposited 2022-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1077–1390（314 aa）	Mutation：F1077A, R1079A	XJI (3P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-3-(4-chloro-2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M di-Ammonium Citrate	Resolution 1.55 Å R-free 0.209
8F8E Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound Deposited 2022-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1077–1390（314 aa）	Mutation：F1077A, R1079A	XJI (3P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-3-(4-chloro-2-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M di-Ammonium Citrate	Resolution 1.55 Å R-free 0.209
8OG5 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1 Deposited 2023-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1039–1401（363 aa）	Mutation：Q1250L	EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 LQH 5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate	Resolution 2.20 Å R-free 0.235
8OG6 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1 Deposited 2023-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1039–1401（363 aa）	Mutation：Q1250L	LQH 5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Tris pH 7.0, 2.13M Lithium acetate	Resolution 2.25 Å R-free 0.231
8OG7 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 2 Deposited 2023-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1039–1401（363 aa）	Mutation：Q1250L	ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 VMR (4~{R})-4-[3-(4-chloranylphenoxy)phenyl]pyrrolidin-2-imine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate	Resolution 2.64 Å R-free 0.206
8OG8 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 3 Deposited 2023-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1039–1401（363 aa）	Mutation：Q1250L	VM8 5-(2-methyl-1-phenyl-propan-2-yl)imidazo[2,1-a]isoquinoline × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate	Resolution 2.11 Å R-free 0.212
8OG9 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 4 Deposited 2023-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1039–1401（363 aa）	Mutation：Q1250L	VM3 5-[1-(4-chlorophenyl)cyclopropyl]imidazo[2,1-a]isoquinoline × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 2.13M Lithium acetate	Resolution 2.94 Å R-free 0.240
8OGA Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 6 Deposited 2023-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain P 1079–1393（315 aa）	Mutation：Q1250L	EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 2 VLW 5-[1-(4-methoxyphenyl)cyclopropyl]-8-(4-methylpiperazin-1-yl)-2,3-dihydroimidazo[2,1-a]isoquinoline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M Tris pH 7.5, 1.66M Lithium acetate	Resolution 2.20 Å R-free 0.209
8OGB Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 8 Deposited 2023-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1039–1401（363 aa）	Mutation：Q1250L	EDO 1,2-ETHANEDIOL × 1 VN5 ~{N}'-[2-[1-(4-methoxyphenyl)cyclopropyl]-7-(4-methylpiperazin-1-yl)quinazolin-4-yl]ethane-1,2-diamine × 1 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M Tris pH 7.5, 2.13M Lithium acetate	Resolution 2.27 Å R-free 0.212
8OGC Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 11 Deposited 2023-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1039–1401（363 aa）	Mutation：Q1250L	DMS DIMETHYL SULFOXIDE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 1 VMZ 1-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclopentyl]quinazolin-7-yl]piperazin-1-yl]ethanone × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M Tris pH 7.5, 2.18M Lithium acetate	Resolution 2.09 Å R-free 0.202
8OO5 Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 13 Deposited 2023-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain P 1079–1393（315 aa）	Mutation：Q1250L	VUF 1-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclohexyl]quinazolin-7-yl]piperazin-1-yl]ethanone × 2 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.91M LiSO4, 0.1M Tris pH 7.5	Resolution 2.25 Å R-free 0.220
8OOD Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15 Deposited 2023-04-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1039–1401（363 aa）	Mutation：Q1250L	MG MAGNESIUM ION × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 5 VY3 ~{N}-[2-[2-[2-[2-[2-[2-[3-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclopentyl]quinazolin-7-yl]piperazin-1-yl]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]ethanamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.13M LiSO4, 0.1M Tris pH 7.5	Resolution 1.50 Å R-free 0.186
9B9H Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40333 Deposited 2024-04-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1080–1390（311 aa） Fragment：residues 1080-1390	Not recorded	A1AM2 N-{(1P)-5'-({(17E)-18-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-16-oxo-3,6,9,12-tetraoxa-15-azaoctadec-17-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；5% w/v 1-ethyl-3-methylimidazolium ethyl sulfate, 15% w/v polyethylene glycol 20,000, pH 7.9	Resolution 2.06 Å R-free 0.229
9B9T Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40407 Deposited 2024-04-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1080–1390（311 aa） Fragment：residues 1080-1390	Not recorded	A1ANM N-{(1P)-5'-[(17-{(4P)-4-[(2P)-4-{[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-1H-pyrazol-1-yl}-16-oxo-3,6,9,12-tetraoxa-15-azaheptadecan-1-yl)carbamoyl]-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate trihydrate, pH 4.6, 2.0 M sodium formate	Resolution 2.05 Å R-free 0.196
9B9W Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40792 Deposited 2024-04-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1080–1390（311 aa） Fragment：residues 1080-1390	Not recorded	A1ANN (4P)-N-[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(25E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,24-dioxo-5,8,11,14,17,20-hexaoxa-2,23-diazahexacos-25-en-26-yl]-1H-pyrrole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；35% v/v tacsimate, pH 7.0	Resolution 1.92 Å R-free 0.183
9BA2 Crystal structure of the binary complex of DCAF1 and WDR5 Deposited 2024-04-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1080–1390（311 aa） Fragment：residues 1080-1390	Not recorded	IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M imidazole, pH 7.4, 20% w/v polyethylene glycol 4,000	Resolution 2.97 Å R-free 0.266
9BHR Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound Deposited 2024-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1077–1390（314 aa）	Not recorded	A1API (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(2-methoxyethyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Magnesium formate	Resolution 1.62 Å R-free 0.187
9BHR Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound Deposited 2024-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1077–1390（314 aa）	Not recorded	A1API (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(2-methoxyethyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Magnesium formate	Resolution 1.62 Å R-free 0.187
9BHS Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound Deposited 2024-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1077–1390（314 aa）	Not recorded	A1APJ (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrole-3-carboxamide × 1 UNL UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide	Resolution 1.43 Å R-free 0.170
9BHS Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound Deposited 2024-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1077–1390（314 aa）	Not recorded	A1APJ (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrole-3-carboxamide × 1 UNL UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide	Resolution 1.43 Å R-free 0.170
9C1Q Crystal structure of the WDR domain of human DCAF1 in complex with OICR-39512 compound Deposited 2024-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1077–1390（314 aa）	Not recorded	A1ATT (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(3-methoxyprop-1-yn-1-yl)-1H-pyrrole-3-carboxamide × 1 UNX UNKNOWN LIGAND × 4 NA SODIUM ION × 2 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Magnesium formate	Resolution 1.80 Å R-free 0.191
9D4E Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103 Deposited 2024-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1077–1390（314 aa）	Not recorded	A1A1Q (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M di-Ammonium Citrate	Resolution 1.70 Å R-free 0.206
9D4E Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103 Deposited 2024-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1077–1390（314 aa）	Not recorded	A1A1Q (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M di-Ammonium Citrate	Resolution 1.70 Å R-free 0.206
9DLW Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41114 Deposited 2024-09-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1080–1390（311 aa） Fragment：residues 1080-1390	Not recorded	A1BAF N-{(1P)-5'-({(32E)-33-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-31-oxo-3,6,9,12,15,18,21,24,27-nonaoxa-30-azatritriacont-32-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；294 K；1.8 M Sodium phosphate monobasic monohydrate, potassium phosphate dibasic / pH 6.9	Resolution 2.07 Å R-free 0.242
9NSN Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41059 Deposited 2025-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1080–1390（311 aa） Fragment：residues 1080-1390	Not recorded	A1B0X N-{(1P)-5'-({(26E)-27-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-25-oxo-3,6,9,12,15,18,21-heptaoxa-24-azaheptacos-26-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-5,6-dihydropyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.15 M cesium chloride, 15% PEG3350	Resolution 1.85 Å R-free 0.234
9NSO Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41060 Deposited 2025-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1080–1390（311 aa） Fragment：residues 1080-1390	Not recorded	A1B0Y (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(34E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,33-dioxo-5,8,11,14,17,20,23,26,29-nonaoxa-2,32-diazapentatriacont-34-en-35-yl]-1H-pyrrole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M sodium citrate tribasic dihydrate, pH 4.2, 0.4 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic monohydrate	Resolution 1.85 Å R-free 0.218
9PLY Crystal structure of the human DCAF1 WDR domain in complex with OICR-40156 Deposited 2025-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1077–1390（314 aa） Chain B 1077–1390（314 aa）	Not recorded	A1CI0 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(3-methoxypropyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide × 2 EDO 1,2-ETHANEDIOL × 2 UNX UNKNOWN LIGAND × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M Magnesium formate	Resolution 1.40 Å R-free 0.174
9Y4Q Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102 Deposited 2025-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1077–1390（314 aa） Chain B 1077–1390（314 aa）	Not recorded	A1CR9 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(pyrimidin-5-yl)-1H-pyrrole-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；3.2 M NaCl, 0.1 M Bis-Tris Propane pH 7.0	Resolution 1.48 Å R-free 0.193
9Y76 Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120 Deposited 2025-09-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1077–1390（314 aa）	Not recorded	A1CSX (4P,5M)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{1-[2-(morpholin-4-yl)ethyl]-1H-pyrazol-4-yl}-1H-pyrrole-3-carboxamide × 1 UNX UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M magnesium formate	Resolution 1.56 Å R-free 0.208
9Y76 Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120 Deposited 2025-09-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1077–1390（314 aa）	Not recorded	A1CSX (4P,5M)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{1-[2-(morpholin-4-yl)ethyl]-1H-pyrazol-4-yl}-1H-pyrrole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M magnesium formate	Resolution 1.56 Å R-free 0.208
9YDG Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074 Deposited 2025-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1080–1390（311 aa）	Not recorded	A1CU7 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-(morpholin-4-yl)-3-oxoprop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M Potassium Fluoride	Resolution 1.54 Å R-free 0.218
9YDG Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074 Deposited 2025-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1080–1390（311 aa）	Not recorded	A1CU7 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-(morpholin-4-yl)-3-oxoprop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% w/v PEG 3350, 0.2 M Potassium Fluoride	Resolution 1.54 Å R-free 0.218
9YE4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41110 Deposited 2025-09-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1080–1390（311 aa）	Not recorded	A1CVQ (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% w/v PEG 3350, 0.1 M Ammonium Sulphate, 0.1 M Bis-Tris pH 5.5	Resolution 1.74 Å R-free 0.224
9YE4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41110 Deposited 2025-09-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1080–1390（311 aa）	Not recorded	A1CVQ (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% w/v PEG 3350, 0.1 M Ammonium Sulphate, 0.1 M Bis-Tris pH 5.5	Resolution 1.74 Å R-free 0.224
9YV4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41109 Deposited 2025-10-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1080–1390（311 aa）	Not recorded	A1CY9 (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(pyrrolidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 NA SODIUM ION × 1 UNX UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% w/v PEG 3350, 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5	Resolution 1.60 Å R-free 0.194
9YV4 Crystal structure of the human DCAF1 WDR domain in complex with OICR-41109 Deposited 2025-10-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1080–1390（311 aa）	Not recorded	A1CY9 (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(pyrrolidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% w/v PEG 3350, 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5	Resolution 1.60 Å R-free 0.194
9ZL9 Crystal structure of DCAF1 in complex with SDIPTAC C7 Deposited 2025-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1077–1390（314 aa） Chain B 1077–1390（314 aa） Chain C 1077–1390（314 aa） Chain D 1077–1390（314 aa） Chain E 1077–1390（314 aa） Chain F 1077–1390（314 aa）	Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A	A1C24 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide × 4 A1C23 (4P,4'P)-5,5'-[(1E,30E)-3,29-dioxo-7,10,13,16,19,22,25-heptaoxa-4,28-diazahentriaconta-1,30-diene-1,31-diyl]bis{N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide} × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；294.15 K；0.2 M sodium fluoride, 20% w/v PEG 3350, pH 7.3	Resolution 2.60 Å R-free 0.317
9ZLE Crystal structure of DCAF1 in complex with SDIPTAC C8 Deposited 2025-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1077–1390（314 aa） Chain B 1077–1390（314 aa） Chain C 1077–1390（314 aa） Chain D 1077–1390（314 aa） Chain E 1077–1390（314 aa） Chain F 1077–1390（314 aa）	Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A	A1C24 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide × 4 A1C25 (4P,4'P)-5,5'-[(1E,33E)-3,32-dioxo-7,10,13,16,19,22,25,28-octaoxa-4,31-diazatetratriaconta-1,33-diene-1,34-diyl]bis{N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide} × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；294.15 K；1.0 M ammonium tartrate dibasic, 0.1 M sodium acetate trihydrate, pH 4.6	Resolution 2.55 Å R-free 0.305
9ZLG Crystal structure of DCAF1 in complex with SDIPTAC C9 Deposited 2025-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1077–1390（314 aa） Chain B 1077–1390（314 aa） Chain C 1077–1390（314 aa） Chain D 1077–1390（314 aa） Chain E 1077–1390（314 aa） Chain F 1077–1390（314 aa） Chain G 1077–1390（314 aa） Chain H 1077–1390（314 aa）	Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A	A1C24 (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide × 4 A1C26 (4P,4'P)-5,5'-[(1E,36E)-3,35-dioxo-7,10,13,16,19,22,25,28,31-nonaoxa-4,34-diazaheptatriaconta-1,36-diene-1,37-diyl]bis{N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide} × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；5% w/v 1-ethyl-3-methylimidazolium acetate, 15% w/v PEG 20,000, pH 6.5	Resolution 2.30 Å R-free 0.289
9ZLI Crystal structure of DCAF1 in complex with SDIPTAC C11 Deposited 2025-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1077–1390（314 aa） Chain B 1077–1390（314 aa） Chain C 1077–1390（314 aa） Chain D 1077–1390（314 aa） Chain E 1077–1390（314 aa） Chain F 1077–1390（314 aa）	Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A Mutation：F1077A, R1079A	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.07 Å R-free 0.278

46 other PDB entries and 59 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPRBP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–341； UniProt 1057–1396 Author chain D； PDBConstruct 2–341； UniProt 1057–1396

Vpx protein

Simian immunodeficiency virus

UniProt Q7ZB17

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–89	Not recorded	Protein VPRBP × 1 （Q9Y4B6） SAM domain and HD domain-containing protein × 1 （H6WEA4） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2	Resolution 2.60 Å R-free 0.228
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 1–89	Not recorded	Protein VPRBP × 1 （Q9Y4B6） SAM domain and HD domain-containing protein × 1 （H6WEA4） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2	Resolution 2.60 Å R-free 0.228

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4Z8L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5AJA Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) bound to Vpx isolated from mandrill and human DCAF1 (amino acid residues 1058-1396) Deposited 2015-02-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–99（99 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.16 M TRISODIUM CITRATE-HCL PH 5.2, 4% PEG 6000	Resolution 2.65 Å R-free 0.227

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q7ZB17_SIV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–92； UniProt 1–89 Author chain E； PDBConstruct 4–92； UniProt 1–89

SAM domain and HD domain-containing protein

Mandrillus sphinx

UniProt H6WEA4

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–115	Fragment：N-terminal	Protein VPRBP × 1 （Q9Y4B6） Vpx protein × 1 （Q7ZB17） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2	Resolution 2.60 Å R-free 0.228
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 1–115	Fragment：N-terminal	Protein VPRBP × 1 （Q9Y4B6） Vpx protein × 1 （Q7ZB17） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M Sodium Phosphate/Citrate buffer, pH 4.2	Resolution 2.60 Å R-free 0.228

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4Z8L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5AJA Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) bound to Vpx isolated from mandrill and human DCAF1 (amino acid residues 1058-1396) Deposited 2015-02-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–114（114 aa） Fragment：N-TERMINAL DOMAIN, UNP 1-114	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.16 M TRISODIUM CITRATE-HCL PH 5.2, 4% PEG 6000	Resolution 2.65 Å R-free 0.227

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H6WEA4_MANSP
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–118； UniProt 1–115 Author chain F； PDBConstruct 4–118； UniProt 1–115

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4z8l
Deposition date deposition_date	2015-04-09
Structure title title	Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex
Keywords keywords	HIV, antiviral defense, Viral Protein-VPX-BINDING PROTEIN complex; Viral Protein/VPX-BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.12 Å
Radius of gyration Rg (electron density) rg_electron	32.58 Å
Forward intensity I(0) i0	197338000.00
Molecular weight molecular_weight	109670.0 kDa
Excluded volume excluded_volume	135940 Å³
Envelope volume envelope_volume	175470 Å³
Hydration-shell volume shell_volume	44327 Å³
Envelope diameter envelope_diameter	120.0 Å
Shell Rg shell_rg	39.88 Å
Envelope Rg envelope_rg	32.36 Å
Shape Rg shape_rg	32.59 Å
Total Rg total_rg	33.11 Å
Total atoms total_atoms	7714
Residues n_residues	955
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	107.6 Å
Rg (real space) rg_real	33.02 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	1.9730e+08
I(0) uncertainty (real space) i0_real_error	2.8940e+06
Rg (reciprocal space) rg_reciprocal	33.07 Å
I(0) (reciprocal space) i0_reciprocal	197300000.0000
Solution quality estimate total_estimate	0.8986
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.1 Å
Skewness Skewness skewness	0.227
Kurtosis Kurtosis kurtosis	-0.473
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	54010000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protein VPRBP
Molecular weight formula_weight	39777.7 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	7828

ARASFPKYGGVDGGCFDRHLIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVGRQRLAELEHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Baculoviridae

Entity 2 Entity 2 polymer

Description description	Vpx protein
Molecular weight formula_weight	12204.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

SEFMAERAPEAPEGAGEVGLEQWLETSLERINREARLHFHPEFLFRLWNTCVEHWHDRHQRSLDYAKYRYLLLMHKAMYTHMQQGCPCRNGRLEHHHHHH

来源 Source

来源生物 organism	Simian immunodeficiency virus
通用名 common_name	SIV
NCBI Class编号 ncbi_taxonomy_id	11723
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	SAM domain and HD domain-containing protein
Molecular weight formula_weight	13197.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

SEFMQQADSDQPSKRPRFDDSPRTPSSTPSAEADCSPGVELHPDYKTWGPEQVCFFLRRGGFGEPALLKNIRENKITGALLPCLDESHFENLGVSSLGERKKLLSYIQRSGQIHVDTM

来源 Source

来源生物 organism	Mandrillus sphinx
通用名 common_name	Mandrill
NCBI Class编号 ncbi_taxonomy_id	9561
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4z8lA00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	4z8lB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4730 —

Domain ID domain_id	4z8lD00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	4z8lE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4730 —

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8. Citations (1)

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Unit-cell length a length_a	74.490 Å
Unit-cell length b length_b	74.490 Å
Unit-cell length c length_c	178.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	43.695 Å
R factor r_factor	0.2015
R_work r_work	0.1992
R_free r_free	0.2277

fit	/app/data/saxs_computation/z8/4z8l/4z8l.fit
pddf	/app/data/pr_computation/z8/4z8l/4z8l.pr.out
profile	/app/data/saxs_computation/z8/4z8l/4z8l.dat

Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein VPRBP

State in the Current Structure

Other States of the Same Protein in the Database

Vpx protein

State in the Current Structure

Other States of the Same Protein in the Database

SAM domain and HD domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)