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4o64

Zinc fingers of KDM2B

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysine-specific demethylase 2B

Homo sapiens

UniProt Q8NHM5

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 607–723 Fragment：UNP Residues 607-723 ZN ZINC ION × 4 UNX UNKNOWN LIGAND × 6 X-RAY DIFFRACTION X-ray crystallization conditions：sitting drop；pH 8.5；291 K；25% PEG 8000, 0.2 M sodium chloride, 0.1 M tris, pH 8.5, sitting drop, temperature 291K Resolution 2.13 Å R-free 0.220
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 607–723 Fragment：UNP Residues 607-723 ZN ZINC ION × 4 UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION X-ray crystallization conditions：sitting drop；pH 8.5；291 K；25% PEG 8000, 0.2 M sodium chloride, 0.1 M tris, pH 8.5, sitting drop, temperature 291K Resolution 2.13 Å R-free 0.220
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 607–723 Fragment：UNP Residues 607-723 ZN ZINC ION × 4 UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION X-ray crystallization conditions：sitting drop；pH 8.5；291 K；25% PEG 8000, 0.2 M sodium chloride, 0.1 M tris, pH 8.5, sitting drop, temperature 291K Resolution 2.13 Å R-free 0.220

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 4O64 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5JH5 Structural Basis for the Hierarchical Assembly of the Core of PRC1.1 Deposited 2016-04-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1059–1336（278 aa） Fragment：RESIDUES 1059-1336
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；298 K；100 mM HEPES, 10 % 2-methyl-2,4-pentanediol, 10 mM NaCl
Resolution 2.55 Å R-free 0.257
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 991–1035（45 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
Resolution 2.66 Å R-free 0.263
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 991–1035（45 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
Resolution 2.66 Å R-free 0.263

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KDM2B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–118； UniProt 607–723 Author chain B； PDBConstruct 2–118； UniProt 607–723 Author chain C； PDBConstruct 2–118； UniProt 607–723

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

暂无 SAXS 图

P(r) Distance Distribution P(r) Distribution

暂无 P(r) 图
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4o64
Deposition date deposition_date2013-12-20
Structure title titleZinc fingers of KDM2B
Keywords keywordsCXXC zinc finger, ring zinc finger, Structural Genomics, Structural Genomics Consortium, SGC, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

该条目暂无 SAXS 数据。

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

该条目暂无 P(r) 分析数据。

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4o64A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id4o64B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id4o64C01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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8. Citations (1)

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9. Files and Curves (0)