MolNFT v1 · #179264 · protein

Puromycin N-acetyltransferase in complex with acetyl-CoA

7K09: “Puromycin N-acetyltransferase in complex with acetyl-CoA”. X-ray diffraction, 1 ligand (ACO), 13 pockets (best druggability 0.84). MolNFT v1 #179264 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7K09
Type: protein
Length: 1,164 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Puromycin N-acetyltransferase
EC: 2.3.-.-
UniProt: P13249
Ligands: ACO
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Puromycin N-acetyltransferase (EC 2.3.-.-)	protein	194	52% helix, 20% strand	P13249
B	Puromycin N-acetyltransferase (EC 2.3.-.-)	protein	192	52% helix, 20% strand	P13249
D, F	Puromycin N-acetyltransferase (EC 2.3.-.-)	protein	195	49% helix, 21% strand	P13249

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

13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	917	0.84	0.85	100	ACO
2	1102	0.81	0.82	83	ACO
3	760	0.81	0.84	63	ACO
4	1025	0.81	0.82	85	ACO
5	511	0.81	0.87	45	ACO

Interfaces

8 interfaces between chains.

A–D · 518 Å² buried · 5 hydrogen bonds · protein-protein
C–F · 462 Å² buried · 10 hydrogen bonds · protein-protein
D–F · 417 Å² buried · 1 hydrogen bond · protein-protein
A–C · 366 Å² buried · 1 hydrogen bond · protein-protein
A–B · 354 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7K09 · Puromycin N-acetyltransferase in complex with acetyl-CoA · the same entry in another collection · chain F against F, TM-score 1.00
P13249 · AlphaFold monomer V2.0 prediction for puromycin N-acetyltransferase (P13249) · a predicted model of the same protein · chain B 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 P13249
Elsewhere: RCSB PDB 7K09 · PDBe 7K09 · UniProt P13249

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