8OOD: Human DCAF1 WD40 repeats

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15. Determined by X-ray diffraction at 1.5 Å resolution. Released 24 May 2023.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,022
Mol. weight: 43.87 kDa
Ligands: MG, VY3
Released: 24 May 2023

Explore 8OOD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OOD contains 3 α-helices and 28 β-strands across 1 chain. 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, 28 β-strands

Element	Residues	Length	Sheet
β-strand	1081-1087	7	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	1229-1230	2	5
β-strand	1236-1239	4	5
β-strand	1242-1245	4	5
β-strand	1250-1254	5	5
α-helix	1255-1257	3
β-strand	1265-1266	2	6
β-strand	1272-1275	4	6
β-strand	1278-1281	4	6
β-strand	1287-1290	4	6
α-helix	1292-1294	3
β-strand	1297-1301	5	7
β-strand	1307-1313	7	7
α-helix	1314	1
β-strand	1330-1338	9	7
β-strand	1344-1349	6	7
β-strand	1353-1359	7	1
β-strand	1365-1371	7	1
β-strand	1382-1388	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DDB1- and CUL4-associated factor 1	A	protein	367	Homo sapiens	Q9Y4B6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8OOD_1 DDB1- and CUL4-associated factor 1 (chains A)
GGGREPKQRRQAPINFTSRLNRRASFPKYGGVDGGCFDRHLIFSRFRPISVFREANEDES
GFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSA
TWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTL
FNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSALAIHKFDKFNMNISGVFHPNGLEVI
INTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSF
RTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVGRQRL
AEDEDEE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
VY3	~{N}-[2-[2-[2-[2-[2-[2-[3-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclo…	C42 H62 Cl N7 O8	2

Water and common crystallization additives (ACT, EDO) are not listed.

Primary citation

Reinstating targeted protein degradation with DCAF1 PROTACs in CRBN PROTAC resistant settings. Schroder, M., Renatus, M., Thoma, C.R. bioRxiv (2023). DOI 10.1101/2023.04.09.536153

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
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
9D4E 1.7 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103
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

Browse structure collections

About this viewer

MolViewer shows 8OOD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.