MolNFT v1 · #115636 · protein

The crystal structure of xenobiotic reductase a (xena) from pseudomonas putida in complex with a nicotinamide mimic (MNH2)

5CPL: “The crystal structure of xenobiotic reductase a (xena) from pseudomonas putida in complex with a nicotinamide…”. X-ray diffraction, 3 ligands (536, FNR, CA), 4 pockets (best druggability 0.78). MolNFT v1 #115636 on GenesisL1: 3D…

PDB: 5CPL
Type: protein
Length: 718 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xenobiotic reductase
UniProt: Q9R9V9
Ligands: 536, FNR, CA
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Xenobiotic reductase	protein	359	40% helix, 16% strand	Q9R9V9

Ligands and binding sites

536 · 1-benzyl-1,4,5,6-tetrahydropyridine-3-carboxamide · ligand · 2 copies · chains A, B
FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · chains B

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

Pockets

4 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	545	0.78	0.84	48	536, FNR
2	541	0.77	0.84	58	536, FNR
3	93	0.39	0.76	22	empty
4	76	0.32	0.74	25	empty

Interfaces

1 interface between chains.

A–B · 1370 Å² buried · 12 hydrogen bonds · protein-protein

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 Q9R9V9
Elsewhere: RCSB PDB 5CPL · PDBe 5CPL · UniProt Q9R9V9

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