MolNFT v1 · #48499 · protein

Oxidized penicillin V acylase from B. sphaericus

2PVA: “Oxidized penicillin V acylase from B. sphaericus”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #48499 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PVA
Type: protein
Length: 1,328 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penicillin V acylase
EC: 3.5.1.11
UniProt: P12256
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Penicillin V acylase (EC 3.5.1.11)	protein	332	20% helix, 33% strand	P12256

Ligands and binding sites

DTD · Dithiane diol · additive · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	457	0.86	0.93	93	empty
2	151	0.82	0.98	37	empty
3	129	0.79	0.98	38	empty
4	127	0.78	0.96	19	DTD
5	117	0.78	0.96	21	DTD

Interfaces

6 interfaces between chains.

B–C · 3285 Å² buried · 39 hydrogen bonds · protein-protein
A–D · 3276 Å² buried · 39 hydrogen bonds · protein-protein
C–D · 1290 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1239 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 376 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

2PVA · Oxidized penicillin V acylase from B. sphaericus · the same entry in another collection · chain A against A, TM-score 1.00
P12256 · AlphaFold monomer V2.0 prediction for penicillin acylase (P12256) · a predicted model of the same protein · chain A 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 P12256
Elsewhere: RCSB PDB 2PVA · PDBe 2PVA · UniProt P12256

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