9EKP: WDR55

Crystal structure of WDR55 in complex with XS381774. Determined by X-ray diffraction at 1.95 Å resolution. Released 10 Dec 2025.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,101
Mol. weight: 69.52 kDa
Ligands: A1BI5
Released: 10 Dec 2025

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

Secondary structure: helices and β-sheets

9EKP contains 8 α-helices and 62 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: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	1
α-helix	32-34	3
β-strand	35-36	2	2
α-helix	37	1
β-strand	41-46	6	3
β-strand	52-57	6	3
β-strand	62-66	5	3
β-strand	70	1	1
β-strand	75-80	6	3
β-strand	87-92	6	4
β-strand	98-103	6	4
β-strand	108-112	5	4
β-strand	118-122	5	4
β-strand	130-137	8	5
β-strand	140-145	6	5
β-strand	150-154	5	5
β-strand	162-164	3	5
β-strand	171-176	6	6
β-strand	182-187	6	6
β-strand	192-196	5	6
β-strand	201-205	5	6
α-helix	212	1
β-strand	213-219	7	7
β-strand	224-229	6	7
β-strand	233-238	6	7
β-strand	241	1	7
β-strand	247-250	4	7
β-strand	258-261	4	8
β-strand	266-270	5	8
β-strand	275-280	6	8
β-strand	285-292	8	8
β-strand	298-303	6	2
β-strand	309-314	6	2
β-strand	318-323	6	2
α-helix	325-330	6

Chain B: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	9
α-helix	32-34	3
β-strand	35-36	2	10
β-strand	41-46	6	11
β-strand	52-57	6	11
β-strand	62-66	5	11
β-strand	70	1	9
β-strand	75-80	6	11
β-strand	87-92	6	12
β-strand	98-103	6	12
β-strand	108-112	5	12
β-strand	118-122	5	12
β-strand	130-137	8	13
β-strand	140-145	6	13
β-strand	150-154	5	13
β-strand	162-164	3	13
β-strand	171-176	6	14
β-strand	182-187	6	14
β-strand	192-196	5	14
β-strand	201-205	5	14
α-helix	206-209	4
α-helix	212	1
β-strand	213-219	7	15
β-strand	224-229	6	15
β-strand	233-238	6	15
β-strand	241	1	15
β-strand	247-250	4	15
β-strand	258-261	4	16
β-strand	266-270	5	16
β-strand	275-280	6	16
β-strand	285-292	8	16
β-strand	298-303	6	10
β-strand	309-314	6	10
β-strand	318-323	6	10
α-helix	324-330	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
WD repeat-containing protein 55	A, B	protein	314	Homo sapiens	Q9H6Y2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9EKP_1 WD repeat-containing protein 55 (chains A, B)
SMEAPTRIRDTPEDIVLEAPASGLAFHPARDLLAAGDVDGDVFVFSYSCQEGETKELWSS
GHHLKACRAVAFSEDGQKLITVSKDKAIHVLDVEQGQLERRVSKAHGAPINSLLLVDENV
LATGDDTGGIRLWDQRKEGPLMDMRQHEEYIADMALDPAKKLLLTASGDGCLGIFNIKRR
RFELLSEPQSGDLTSVTLMKWGKKVACGSSEGTIYLFNWNGFGATSDRFALRAESIDCMV
PVTESLLCTGSTDGVIRAVNILPNRVVGSVGQHTGEPVEELALSHCGRFLASSGHDQRLK
FWDMAQLRAVVVDD

Ligands and cofactors

ID	Name	Formula	Copies
A1BI5	(7P,8S)-7-[(2S)-2-methyl-2,3-dihydro-1-benzofuran-5-yl][1,2,4]triazolo[1,5-a]py…	C14 H12 N4 O	2

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

Primary citation

Crystal structure of WDR55 in complex with XS381774. Chen, U.H., Li, F., Zeng, H. et al. To be published.

Other PDB entries of the same protein (UniProt Q9H6Y2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KQQ 1.8 Å, Crystal structure of human WDR55
8FKY 2.67 Å, Human nucleolar pre-60S ribosomal subunit (State F)

Browse structure collections

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