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Crystal structure of VAT(D) in complex with acetyl-CoA

Analyse Crystal structure of VAT(D) in complex with acetyl-CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KK4
Type: protein
Length: 1,233 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptogramin a acetyltransferase
EC: 2.3.1.-
UniProt: P50870
Ligands: ACO
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Streptogramin a acetyltransferase (EC 2.3.1.-)	protein	205	25% helix, 20% strand	P50870
D, E, F	Streptogramin a acetyltransferase (EC 2.3.1.-)	protein	206	25% helix, 21% strand	P50870

Ligands and binding sites

ACO · Acetyl coenzyme *A · ligand · 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

8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	523	0.74	0.82	61	ACO
2	526	0.73	0.81	58	ACO
3	542	0.73	0.81	57	ACO
4	543	0.73	0.81	58	ACO
5	540	0.72	0.80	58	ACO

Interfaces

6 interfaces between chains.

D–F · 1359 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1338 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1331 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1331 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1324 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1KK4 · Crystal Structure of Vat(D) in Complex with Acetyl-CoA · the same entry in another collection · chain F against F, TM-score 1.00
P50870 · AlphaFold monomer V2.0 prediction for streptogramin a acetyltransferase (P50870) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P50870
Elsewhere: RCSB PDB 1KK4 · PDBe 1KK4 · UniProt P50870

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