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Crystal structure of a soluble variant of full-length human APOBEC3G (pH 9.0)

Analyse Crystal structure of a soluble variant of full-length human APOBEC3G (pH 9.0) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WMC
Type: protein + DNA
Length: 364 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apolipoprotein B mRNA editing enzyme, catalytic peptide-3 like 3G; DNA (5'-D(P*CP*C)-3')
Ligands: ZN
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apolipoprotein B mRNA editing enzyme, catalytic peptide-3 like 3G	protein	362	37% helix, 23% strand	—
B	DNA (5'-D(PCPC)-3')	dna	2	—	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	600	0.75	0.82	54	empty
2	71	0.57	0.88	16	ZN
3	97	0.49	0.82	20	empty

Interfaces

1 interface between chains.

A–B · 347 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

6WMC · Crystal structure of a soluble variant of full-length human APOBEC3G (pH 9.0) · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6WMC · PDBe 6WMC

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