Research workbench

Penicillin acylase, mutant complexed with ppa

Analyse Penicillin acylase, mutant complexed with ppa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1K5S
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: GRO, CA
Pockets: 8 · best druggability 0.67

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	61% helix, 6% strand	P06875
B	Penicillin G acylase beta subunit (EC 3.5.1.11)	protein	557	25% helix, 26% strand	P06875

Ligands and binding sites

GRO · R-2-phenyl-proprionic 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

8 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	65	0.67	0.95	19	empty
2	459	0.66	0.78	50	GRO
3	170	0.46	0.75	28	empty
4	119	0.40	0.75	23	empty
5	97	0.39	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 7206 Å² buried · 122 hydrogen bonds · protein-protein

Compared structures

1K5S · Penicillin acylase, mutant complexed with ppa · 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 1K5S · PDBe 1K5S · UniProt P06875

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