MolNFT v1 · #12079 · protein

Penicillin acylase, mutant complexed with paa

1K5Q · Penicillin G acylase alpha subunit: “Penicillin acylase, mutant complexed with paa”. X-ray diffraction, 2 ligands (PAC, CA), 7 pockets (best druggability 0.69). MolNFT v1 #12079 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1K5Q
Type: protein
Length: 763 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penicillin G acylase alpha subunit; Penicillin G acylase beta subunit
EC: 3.5.1.11
UniProt: P06875
Ligands: PAC, CA
Pockets: 7 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Penicillin G acylase alpha subunit (EC 3.5.1.11)	protein	206	59% helix, 6% strand	P06875
B	Penicillin G acylase beta subunit (EC 3.5.1.11)	protein	557	26% helix, 27% strand	P06875

Ligands and binding sites

PAC · 2-phenylacetic acid · ligand · chains A, B
CA · Calcium ion · metal · chains A, B

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

Pockets

7 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	62	0.69	0.96	19	empty
2	476	0.66	0.78	52	PAC
3	123	0.42	0.76	20	empty
4	118	0.42	0.76	21	empty
5	123	0.38	0.74	21	empty

Interfaces

1 interface between chains.

A–B · 7160 Å² buried · 125 hydrogen bonds · protein-protein

Compared structures

1K5Q · Penicillin acylase, mutant complexed with paa · the same entry in another collection · chain A against A, TM-score 1.00
P06875 · AlphaFold monomer V2.0 prediction for penicillin G acylase (P06875) · 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 P06875
Elsewhere: RCSB PDB 1K5Q · PDBe 1K5Q · UniProt P06875

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