MolNFT v1 · #135858 · protein

A circularly permuted version of pvdq (cppvdq)

5UBL · Acyl-homoserine lactone acylase pvdq: “A circularly permuted version of pvdq (cppvdq)”. X-ray diffraction, 7 pockets (best druggability 0.79). MolNFT v1 #135858 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5UBL
Type: protein
Length: 718 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-homoserine lactone acylase pvdq
EC: 3.5.1.97
UniProt: Q9I194
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acyl-homoserine lactone acylase pvdq (EC 3.5.1.97)	protein	718	33% helix, 26% strand	Q9I194

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	98	0.79	0.98	21	empty
2	579	0.64	0.75	69	empty
3	213	0.46	0.74	32	empty
4	111	0.44	0.78	19	empty
5	148	0.40	0.74	22	empty

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5UBL · A circularly permuted version of PvdQ (cpPvdQ) · the same entry in another collection · chain A against A, TM-score 1.00
Q9I194 · AlphaFold monomer V2.0 prediction for acyl-homoserine lactone acylase pvdq (Q9I194) · a predicted model of the same protein · chain A against A, TM-score 0.76

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 Q9I194
Elsewhere: RCSB PDB 5UBL · PDBe 5UBL · UniProt Q9I194

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