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Crystal structure of human APOBEC3B N-terminal domain

Analyse Crystal structure of human APOBEC3B N-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TKM
Type: protein
Length: 368 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA dc->du-editing enzyme apobec-3B
EC: 3.5.4.-
UniProt: Q9UH17
Ligands: ZN
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA dc->du-editing enzyme apobec-3B (EC 3.5.4.-)	protein	184	40% helix, 28% strand	Q9UH17

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	177	0.46	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 125 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5TKM · Crystal structure of human APOBEC3B N-terminal Domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9UH17 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3B (Q9UH17) · a predicted model of the same protein · chain B against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9UH17
Elsewhere: RCSB PDB 5TKM · PDBe 5TKM · UniProt Q9UH17

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