MolNFT v1 · #103365 · protein

S1C mutant of penicillin G acylase from kluyvera citrophila

4PEL · Penicillin G acylase subunit alpha: “S1C mutant of penicillin G acylase from kluyvera citrophila”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.80). MolNFT v1 #103365 on GenesisL1: 3D structure, binding sites…

PDB: 4PEL
Type: protein
Length: 3,004 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penicillin G acylase subunit alpha; Penicillin G acylase subunit beta
EC: 3.5.1.11
UniProt: P07941
Ligands: CA
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Penicillin G acylase subunit alpha (EC 3.5.1.11)	protein	194	60% helix, 6% strand	P07941
B, D, F, H	Penicillin G acylase subunit beta (EC 3.5.1.11)	protein	557	25% helix, 27% strand	P07941

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	705	0.80	0.84	81	empty
2	582	0.77	0.84	88	empty
3	421	0.73	0.83	71	empty
4	548	0.71	0.80	64	empty
5	660	0.67	0.76	63	empty

Interfaces

11 interfaces between chains.

G–H · 6792 Å² buried · 110 hydrogen bonds · protein-protein
C–D · 6785 Å² buried · 102 hydrogen bonds · protein-protein
E–F · 6773 Å² buried · 106 hydrogen bonds · protein-protein
A–B · 6767 Å² buried · 111 hydrogen bonds · protein-protein
B–H · 1402 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

4PEL · S1C mutant of Penicillin G acylase from Kluyvera citrophila · the same entry in another collection · chain H against H, TM-score 1.00
P07941 · AlphaFold monomer V2.0 prediction for penicillin G acylase (P07941) · a predicted model of the same protein · chain B 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 P07941
Elsewhere: RCSB PDB 4PEL · PDBe 4PEL · UniProt P07941

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