9D4E: Human DCAF1 WDR domain

Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103. Determined by X-ray diffraction at 1.7 Å resolution. Released 18 Dec 2024.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,149
Mol. weight: 72.53 kDa
Ligands: A1A1Q, CIT
Released: 18 Dec 2024

Explore 9D4E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D4E contains 6 α-helices and 63 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	1081-1086	6	1
β-strand	1096-1101	6	2
β-strand	1107-1112	6	2
β-strand	1116-1121	6	2
β-strand	1127-1132	6	2
β-strand	1138-1143	6	3
β-strand	1149-1154	6	3
β-strand	1161-1165	5	3
β-strand	1171-1176	6	3
β-strand	1181-1184	4	4
β-strand	1191-1196	6	4
β-strand	1199-1204	6	4
β-strand	1210-1214	5	4
β-strand	1225	1	5
β-strand	1229-1230	2	6
β-strand	1236-1239	4	6
β-strand	1242-1245	4	6
β-strand	1250-1254	5	6
α-helix	1255-1257	3
β-strand	1262	1	5
β-strand	1265-1266	2	7
β-strand	1272-1275	4	7
β-strand	1278-1281	4	7
β-strand	1287-1290	4	7
α-helix	1292-1294	3
β-strand	1297-1301	5	8
β-strand	1307-1312	6	8
β-strand	1313	1	9
α-helix	1314	1
β-strand	1330	1	9
β-strand	1333-1338	6	8
β-strand	1344-1349	6	8
β-strand	1354-1359	6	1
β-strand	1365-1371	7	1
β-strand	1382-1388	7	1

Chain B: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	1081-1086	6	10
β-strand	1095	1	10
β-strand	1096-1101	6	11
β-strand	1107-1112	6	11
β-strand	1116-1121	6	11
β-strand	1127-1132	6	11
β-strand	1138-1143	6	12
β-strand	1149-1154	6	12
β-strand	1161-1165	5	12
β-strand	1171-1176	6	12
β-strand	1181-1184	4	13
β-strand	1191-1196	6	13
β-strand	1199-1204	6	13
β-strand	1210-1214	5	13
β-strand	1229-1230	2	14
β-strand	1236-1239	4	14
β-strand	1242-1245	4	14
β-strand	1250-1254	5	14
α-helix	1255-1257	3
β-strand	1265-1266	2	15
β-strand	1272-1275	4	15
β-strand	1278-1281	4	15
β-strand	1287-1290	4	15
α-helix	1292-1294	3
β-strand	1297-1301	5	16
β-strand	1307-1312	6	16
β-strand	1313	1	17
α-helix	1314	1
β-strand	1330	1	17
β-strand	1333-1338	6	16
β-strand	1344-1349	6	16
β-strand	1354-1359	6	10
β-strand	1365-1371	7	10
β-strand	1382-1388	7	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DDB1- and CUL4-associated factor 1	A, B	protein	315	Homo sapiens	Q9Y4B6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9D4E_1 DDB1- and CUL4-associated factor 1 (chains A, B)
GASAFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHN
SAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGT
KGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKF
DKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQA
DDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSM
DALNMDTVCRLYEVG

Ligands and cofactors

ID	Name	Formula	Copies
A1A1Q	(4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-flu…	C28 H26 Cl2 F2 N4 O3	2
CIT	Citric acid	C6 H8 O7	1

Primary citation

Crystal structure of the human DCAF1 WDR domain in complex with OICR-1103. Kimani, S., Dong, A., Li, Y. et al. To be published.

Other PDB entries of the same protein (UniProt Q9Y4B6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PLY 1.4 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-40156
9BHS 1.43 Å, Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound
9Y4Q 1.48 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102
8OOD 1.5 Å, Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15
9YDG 1.54 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074
8F8E 1.55 Å, Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound
9Y76 1.56 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120
9YV4 1.6 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-41109
7SSE 1.62 Å, Crystal structure of the WDR domain of human DCAF1 in complex with CYCA-117-70
9BHR 1.62 Å, Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound
4PXW 1.72 Å, Crystal structure of human DCAF1 WD40 repeats (Q1250L)
9YE4 1.74 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-41110

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