Research workbench

BORF2-APOBEC3BCTD complex

Analyse BORF2-APOBEC3BCTD complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RW6
Type: protein
Length: 1,634 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MALTOSE/MALTODEXTRIN-binding periplasmic protein, ribonucleoside-diphosphate reductase…
EC: 1.17.4.1, 3.5.4.38
UniProt: P03190, Q9UH17
Ligands: ZN
Pockets: 15 · best druggability 0.72

Structure

electron microscopy · 2 distinct chains · 44% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	MALTOSE/MALTODEXTRIN-binding periplasmic protein, ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1)	protein	642	45% helix, 10% strand	P03190
B, D	DNA dc->du-editing enzyme apobec-3B (EC 3.5.4.38)	protein	175	39% helix, 18% strand	Q9UH17

Ligands and binding sites

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

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

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	741	0.72	0.78	79	empty
2	340	0.60	0.77	43	empty
3	348	0.59	0.77	36	empty
4	328	0.59	0.77	43	empty
5	214	0.58	0.80	27	empty

Interfaces

3 interfaces between chains.

C–D · 1183 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1174 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 844 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7RW6 · BORF2-APOBEC3Bctd Complex · 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 D against A, TM-score 0.98

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 P03190
Every structure of UniProt Q9UH17
Elsewhere: RCSB PDB 7RW6 · PDBe 7RW6 · UniProt P03190 · UniProt Q9UH17

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