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Crystal structure of a primate APOBEC3G N-terminal domain

Analyse Crystal structure of a primate APOBEC3G 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: 5K81
Type: protein
Length: 1,131 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apolipoprotein B mRNA editing enzyme, catalytic peptide- like 3G,APOLIPOPROTEIN B mRNA…
UniProt: M1GSK9
Ligands: ZN
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Apolipoprotein B mRNA editing enzyme, catalytic peptide- like 3G,APOLIPOPROTEIN B mRNA editing enzyme, catalytic peptide-like 3G	protein	191	43% helix, 21% strand	M1GSK9
D, E, F	Apolipoprotein B mRNA editing enzyme, catalytic peptide- like 3G,APOLIPOPROTEIN B mRNA editing enzyme, catalytic peptide-like 3G	protein	186	41% helix, 24% strand	M1GSK9

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

9 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	901	0.81	0.83	76	empty
2	932	0.75	0.78	75	empty
3	92	0.43	0.78	13	empty
4	92	0.41	0.78	14	empty
5	83	0.41	0.78	20	empty

Interfaces

7 interfaces between chains.

B–D · 693 Å² buried · 3 hydrogen bonds · protein-protein
A–F · 683 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 678 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 651 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 607 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5K81 · Crystal Structure of a Primate APOBEC3G N-Terminal Domain · 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
Every structure of UniProt M1GSK9
Elsewhere: RCSB PDB 5K81 · PDBe 5K81 · UniProt M1GSK9

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