MolNFT v1 · #12546 · protein

Crystal structure of VAT(D) (form II)

1KK5 · Streptogramin a acetyltransferase: “Crystal structure of VAT(D) (form II)”. X-ray diffraction, 8 pockets (best druggability 0.74). MolNFT v1 #12546 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KK5
Type: protein
Length: 1,236 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
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Streptogramin a acetyltransferase (EC 2.3.1.-)	protein	206	26% helix, 21% strand	P50870

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	542	0.74	0.81	57	empty
2	536	0.73	0.81	60	empty
3	532	0.72	0.80	57	empty
4	592	0.72	0.80	55	empty
5	578	0.72	0.80	58	empty

Interfaces

6 interfaces between chains.

D–F · 1351 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1345 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1339 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 1333 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1329 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1KK5 · Crystal Structure of Vat(D) (Form II) · the same entry in another collection · chain C against C, TM-score 1.00
P50870 · AlphaFold monomer V2.0 prediction for streptogramin a acetyltransferase (P50870) · a predicted model of the same protein · chain A 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 P50870
Elsewhere: RCSB PDB 1KK5 · PDBe 1KK5 · UniProt P50870

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