9pxo

Fem-1 homolog B (FEM1B) in complex with VU0023775

Method: X-RAY DIFFRACTION D_max: 115.8 Å Quality: GOOD

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

Protein fem-1 homolog B

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–337	Not recorded	A1CMX 2-tert-butyl-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；298 K；0.1M HEPES pH 7.5, 0.25% PEG 8000, 1.2 M-1.6 M ammonium sulfate, and 0.05-0.1 M sodium thiocyanate	Resolution 3.05 Å R-free 0.340
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–337	Not recorded	A1CMX 2-tert-butyl-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；298 K；0.1M HEPES pH 7.5, 0.25% PEG 8000, 1.2 M-1.6 M ammonium sulfate, and 0.05-0.1 M sodium thiocyanate	Resolution 3.05 Å R-free 0.340

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 9PXO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6LBF Crystal structure of FEM1B Deposited 2019-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Tris-HCl, pH 8.5, 0.1M Guanidine hydrochloride, 0.8M Potassium sodium tartrate tetrahydrate, 0.5% w/v Polyethylene glycol monomethyl ether 5000	Resolution 3.25 Å R-free 0.253
6LBF Crystal structure of FEM1B Deposited 2019-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–356（356 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Tris-HCl, pH 8.5, 0.1M Guanidine hydrochloride, 0.8M Potassium sodium tartrate tetrahydrate, 0.5% w/v Polyethylene glycol monomethyl ether 5000	Resolution 3.25 Å R-free 0.253
7CNG Structure of CDK5R1 bound FEM1B Deposited 2020-07-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.6M Magnesium sulfate hydrate, 0.1M BIS-TRIS propane pH 6.7	Resolution 3.49 Å R-free 0.267
7CNG Structure of CDK5R1 bound FEM1B Deposited 2020-07-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–337（337 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.6M Magnesium sulfate hydrate, 0.1M BIS-TRIS propane pH 6.7	Resolution 3.49 Å R-free 0.267
7EL6 Structure of SMCR8 bound FEM1B Deposited 2021-04-08	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 1–337（337 aa） Chain B 1–337（337 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Tris pH7.3 4% PEG8000	Resolution 2.80 Å R-free 0.266
8IJ1 Protomer 1 and 2 of the asymmetry trimer of the Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complex Deposited 2023-02-24	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 × 9 PDB declaration: nonameric	Chain D 1–627（627 aa） Chain I 1–627（627 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8JE1 An asymmetry dimer of the Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complexed with BEX2 Deposited 2023-05-15	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 × 9 PDB declaration: nonameric	Chain D 1–627（627 aa） Chain I 1–627（627 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.95 Å
8JE2 Cryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B complexed with FNIP1-FLCN Deposited 2023-05-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–627（627 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.63 Å
8WQA Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1) Deposited 2023-10-11	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 × 12 PDB declaration: dodecameric	Chain B 1–627（627 aa） Chain D 1–627（627 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
8WQB Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 2) Deposited 2023-10-11	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 × 11 PDB declaration: undecameric	Chain F 1–627（627 aa） Chain J 1–627（627 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
8WQC cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1 Deposited 2023-10-11	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 × 12 PDB declaration: dodecameric	Chain A 1–627（627 aa） Chain G 1–627（627 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
8WQD Local refinement of FEM1B bound with the C-degron of CCC89 Deposited 2023-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–627（627 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
8WQE Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1 (conformation 1) Deposited 2023-10-11	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 × 12 PDB declaration: dodecameric	Chain B 1–627（627 aa） Chain D 1–627（627 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
8WQF cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1 (conformation 2) Deposited 2023-10-11	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 × 11 PDB declaration: undecameric	Chain F 1–627（627 aa） Chain J 1–627（627 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
8WQG cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1) Deposited 2023-10-11	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 × 12 PDB declaration: dodecameric	Chain A 1–627（627 aa） Chain G 1–627（627 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.09 Å
8WQH cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 2) Deposited 2023-10-11	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 × 12 PDB declaration: dodecameric	Chain D 1–627（627 aa） Chain H 1–627（627 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.44 Å
8WQI Local refinement of FEM1B bound with the C-degron of CUX1 Deposited 2023-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–627（627 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9J64 Cryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B homodimer complexed with FNIP1 degron Deposited 2024-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain I 1–627（627 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.28 Å
9J77 Cryo-EM structure of CRL2-FEM1B (dimer 1) Deposited 2024-08-18	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 × 12 PDB declaration: 12-meric	Chain F 1–627（627 aa） Chain J 1–627（627 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å
9J78 Cryo-EM structure of CRL2-FEM1B (dimer 2) Deposited 2024-08-18	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 × 12 PDB declaration: 12-meric	Chain F 1–627（627 aa） Chain J 1–627（627 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.88 Å
9J79 Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer) Deposited 2024-08-18	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 × 19 PDB declaration: 19-meric	Chain A 1–627（627 aa） Chain J 1–627（627 aa） Chain O 1–627（627 aa） Chain P 1–627（627 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.08 Å
9J7A local refinement of FEM1B bound with TOM20 (dimer) Deposited 2024-08-18	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 × 6 PDB declaration: hexameric	Chain A 1–627（627 aa） Chain D 1–627（627 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.13 Å
9J7B local refinement of FEM1B bound with TOM20(tetramer) Deposited 2024-08-18	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 × 11 PDB declaration: 11-meric	Chain A 1–627（627 aa） Chain J 1–627（627 aa） Chain O 1–627（627 aa） Chain P 1–627（627 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.12 Å
9JCE local refinement of FEM1B bound with TOM20 Deposited 2024-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–627（627 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.59 Å
9LKX local refinement of FEM1B bound with PLD6 Deposited 2025-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1–627（627 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.76 Å
9LKY Dimer of CRL2-FEM1B bound with PLD6 Deposited 2025-01-17	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 × 11 PDB declaration: 11-meric	Chain F 1–627（627 aa） Chain J 1–627（627 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å
9PQ9 Fem-1 homolog B (FEM1B) in complex with VU0421763 Deposited 2025-07-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa）	Not recorded	A1CI7 6-(propylsulfanyl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.25 % PEG 8000, 1.2-1.6 M Ammonium sulfate, 0.05-0.1 M Sodium thiocyanate	Resolution 2.93 Å R-free 0.304
9PQ9 Fem-1 homolog B (FEM1B) in complex with VU0421763 Deposited 2025-07-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–337（337 aa）	Not recorded	A1CI7 6-(propylsulfanyl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.25 % PEG 8000, 1.2-1.6 M Ammonium sulfate, 0.05-0.1 M Sodium thiocyanate	Resolution 2.93 Å R-free 0.304
9PQA Fem-1 homolog B (FEM1B) in complex with VU0432623 Deposited 2025-07-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa）	Not recorded	A1CI8 (6R)-6-phenyl-1,3-thiazinane-2,4-dione × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.25% PEG 8000, 1.2-1.6 M Ammonium sulfate, 0.05-0.1 M Sodium thiocyanate	Resolution 2.90 Å R-free 0.341
9PQA Fem-1 homolog B (FEM1B) in complex with VU0432623 Deposited 2025-07-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–337（337 aa）	Not recorded	A1CI8 (6R)-6-phenyl-1,3-thiazinane-2,4-dione × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.25% PEG 8000, 1.2-1.6 M Ammonium sulfate, 0.05-0.1 M Sodium thiocyanate	Resolution 2.90 Å R-free 0.341
9PQE Fem-1 homolog B (FEM1B) in complex with VU0412674 Deposited 2025-07-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–337（337 aa）	Not recorded	A1CI9 N-[4-(propan-2-yl)phenyl]pyrazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.25% PEG 8000, 1.2-1.6 M Ammonium sulfate, 0.05-0.1 M Sodium thiocyanate	Resolution 3.10 Å R-free 0.326
9PQE Fem-1 homolog B (FEM1B) in complex with VU0412674 Deposited 2025-07-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–337（337 aa）	Not recorded	A1CI9 N-[4-(propan-2-yl)phenyl]pyrazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.25% PEG 8000, 1.2-1.6 M Ammonium sulfate, 0.05-0.1 M Sodium thiocyanate	Resolution 3.10 Å R-free 0.326
9PW8 Fem-1 homolog B (FEM1B) in complex with VU0417412 Deposited 2025-08-04	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 1–337（337 aa） Chain B 1–337（337 aa）	Not recorded	A1CLY N-(4-fluorophenyl)thiophene-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.25% PEG 8000, 1.2-1.6 M Ammonium sulfate, 0.05-0.1 M Sodium thiocyanate	Resolution 2.80 Å R-free 0.338
9PWJ Fem-1 homolog B (FEM1B) in complex with VU0081201 Deposited 2025-08-04	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 1–337（337 aa） Chain B 1–337（337 aa）	Not recorded	A1CL1 3-(2-oxopyrrolidin-1-yl)benzoic acid × 1 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.25% PEG 8000, 1.2 M-1.6 M ammonium sulfate, and 0.05-0.1 M sodium thiocyanate	Resolution 3.00 Å R-free 0.347
9PXP Fem-1 homolog B (FEM1B) in complex with VU0416476 Deposited 2025-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Not recorded	A1CMY 2-tert-butyl-4,5-dichloropyridazin-3(2H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；0.1M HEPES pH 7.5, 0.25% PEG 8000, 1.2 M-1.6 M ammonium sulfate, and 0.05-0.1 M sodium thiocyanate	Resolution 3.00 Å R-free 0.327

30 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FEM1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–339； UniProt 1–337 Author chain B； PDBConstruct 3–339； UniProt 1–337

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	9pxo
Deposition date deposition_date	2025-08-06
最后修订 last_revision	2025-11-26
Structure title title	Fem-1 homolog B (FEM1B) in complex with VU0023775
Keywords keywords	FEM1B, E3 ligase, ligand, LIGASE; LIGASE
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	32.86 Å
Radius of gyration Rg (electron density) rg_electron	32.93 Å
Forward intensity I(0) i0	156077000.00
Molecular weight molecular_weight	66412.0 kDa
Excluded volume excluded_volume	64041 Å³
Envelope volume envelope_volume	118010 Å³
Hydration-shell volume shell_volume	31735 Å³
Envelope diameter envelope_diameter	121.5 Å
Shell Rg shell_rg	37.15 Å
Envelope Rg envelope_rg	32.62 Å
Shape Rg shape_rg	32.96 Å
Total Rg total_rg	33.14 Å
Total atoms total_atoms	5032
Residues n_residues	672
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	115.8 Å
Rg (real space) rg_real	33.14 Å
Rg uncertainty (real space) rg_real_error	1.13 Å
I(0) (real space) i0_real	1.5610e+08
I(0) uncertainty (real space) i0_real_error	2.6250e+06
Rg (reciprocal space) rg_reciprocal	33.03 Å
I(0) (reciprocal space) i0_reciprocal	156100000.0000
Solution quality estimate total_estimate	0.8448
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.2 Å
Skewness Skewness skewness	0.469
Kurtosis Kurtosis kurtosis	-0.285
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13820000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.731; Smooth: 0.882

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	129.844 Å
Unit-cell length b length_b	129.844 Å
Unit-cell length c length_c	139.967 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	tetragonal

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	47.600 Å
R factor r_factor	0.2879
R_work r_work	0.2847
R_free r_free	0.3397

Description description	Protein fem-1 homolog B
Molecular weight formula_weight	39295.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5032

Fem-1 homolog B (FEM1B) in complex with VU0023775

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

Protein fem-1 homolog B

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Escherichia coli

Description description	2-tert-butyl-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid
Molecular weight formula_weight	247.2 kDa
Source method src_method	syn
Copy count entity_count	2

fit	/app/data/saxs_computation/px/9pxo/9pxo.fit
pddf	/app/data/pr_computation/px/9pxo/9pxo.pr.out
profile	/app/data/saxs_computation/px/9pxo/9pxo.dat