9PQ9: Fem-1 homolog B

Name: PDB 9PQ9: Fem-1 homolog B (FEM1B) in complex with VU0421763
Published: 2025-11-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Fem-1 homolog B (FEM1B) in complex with VU0421763. Determined by X-ray diffraction at 2.93 Å resolution. Released 26 Nov 2025.

Method: X-ray diffraction
Resolution: 2.93 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,071
Mol. weight: 79.49 kDa
Ligands: A1CI7
Released: 26 Nov 2025

Explore 9PQ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PQ9 contains 40 α-helices and 12 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: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
α-helix	17-24	8
α-helix	29-36	8
β-strand	40	1	1
β-strand	46	1	2
β-strand	47	1	1
α-helix	49-55	7
α-helix	59-69	11
β-strand	76-80	5	2
β-strand	85-90	6	2
α-helix	91-97	7
α-helix	101-109	9
α-helix	124-131	8
α-helix	134-141	8
α-helix	157-163	7
α-helix	167-175	9
β-strand	183	1	3
β-strand	189	1	3
α-helix	190-196	7
α-helix	200-208	9
α-helix	222-228	7
α-helix	232-241	10
α-helix	246-262	17
α-helix	269-283	15
α-helix	300-302	3
α-helix	311-315	5
α-helix	321-335	15

Chain B: 20 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
α-helix	17-24	8
α-helix	29-36	8
β-strand	40	1	4
β-strand	46	1	5
β-strand	47	1	4
α-helix	49-55	7
α-helix	59-69	11
β-strand	76-81	6	5
β-strand	84-90	7	5
α-helix	91-97	7
α-helix	101-109	9
α-helix	124-131	8
α-helix	134-141	8
α-helix	157-163	7
α-helix	167-175	9
α-helix	190-196	7
α-helix	200-208	9
α-helix	222-228	7
α-helix	232-239	8
α-helix	246-262	17
α-helix	269-283	15
α-helix	300-302	3
α-helix	311-315	5
α-helix	321-335	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein fem-1 homolog B	A, B	protein	357	Homo sapiens	Q9UK73 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9PQ9_1 Protein fem-1 homolog B (chains A, B)
GHMEGLAGYVYKAASEGKVLTLAALLLNRSESDIRYLLGYVSQQGGQRSTPLIIAARNGH
AKVVRLLLEHYRVQTQQTGTVRFDGYVIDGATALWCAAGAGHFEVVKLLVSHGANVNHTT
VTNSTPLRAACFDGRLDIVKYLVENNANISIANKYDNTCLMIAAYKGHTDVVRYLLEQRA
DPNAKAHCGATALHFAAEAGHIDIVKELIKWRAAIVVNGHGMTPLKVAAESCKADVVELL
LSHADCDRRSRIEALELLGASFANDRENYDIIKTYHYLYLAMLERFQDGDNILEKEVLPP
IHAYGNRTECRNPQELESIRQDRDALHMEGLIVRERILGGGGSGGGSKKRLLLGLDR

Ligands and cofactors

ID	Name	Formula	Copies
A1CI7	6-(propylsulfanyl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one	C8 H10 N4 O S	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Nuclear Magnetic Resonance-based fragment screen of the E3 ligase Fem-1 homolog B. Katinas, J.M., Amporndanai, K., Taylor, A.J. et al. Protein Sci (2025) 34:e70365-e70365. DOI 10.1002/pro.70365 · PubMed

Other PDB entries of the same protein (UniProt Q9UK73 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PW8 2.8 Å, Fem-1 homolog B (FEM1B) in complex with VU0417412
7EL6 2.8 Å, Structure of SMCR8 bound FEM1B
9PQA 2.9 Å, Fem-1 homolog B (FEM1B) in complex with VU0432623
9PWJ 3.0 Å, Fem-1 homolog B (FEM1B) in complex with VU0081201
9PXP 3.0 Å, Fem-1 homolog B (FEM1B) in complex with VU0416476
9PXO 3.05 Å, Fem-1 homolog B (FEM1B) in complex with VU0023775
9PQE 3.1 Å, Fem-1 homolog B (FEM1B) in complex with VU0412674
6LBF 3.25 Å, Crystal structure of FEM1B
8WQF 3.27 Å, cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1…
8WQB 3.37 Å, Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89…
8WQE 3.38 Å, Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1…
8WQA 3.39 Å, Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89…

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