MolNFT v1 · #121901 · protein

Crystal structure of pvdn from pseudomonas aeruginosa

5I90: “Crystal structure of pvdn from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (PLP), 7 pockets (best druggability 0.82). MolNFT v1 #121901 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I90
Type: protein
Length: 780 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pvdn
UniProt: G3XCY5
Ligands: PLP
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pvdn	protein	390	44% helix, 16% strand	G3XCY5

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 5 copies · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	188	0.82	0.97	46	empty
2	430	0.74	0.84	60	PLP
3	384	0.72	0.83	57	PLP, EDO
4	140	0.46	0.77	24	EDO
5	98	0.36	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 2740 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

5I90 · Crystal Structure of PvdN from Pseudomonas Aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00

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 G3XCY5
Elsewhere: RCSB PDB 5I90 · PDBe 5I90 · UniProt G3XCY5

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