MolNFT v1 · #115637 · protein

Xena from pseudomonas putida in complex with NADPH4.

5CPM · Xenobiotic reductase: “Xena from pseudomonas putida in complex with NADPH4.”. X-ray diffraction, 2 ligands (NDP, FNR), 2 pockets (best druggability 0.80). MolNFT v1 #115637 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5CPM
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: NDP, FNR
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Xenobiotic reductase	protein	359	41% helix, 17% strand	Q9R9V9

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · 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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1193	0.80	0.81	103	NDP, FNR
2	79	0.33	0.74	24	empty

Interfaces

1 interface between chains.

A–B · 1364 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5CPM · XenA from Pseudomonas putida in complex with NADPH4. · 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 Q9R9V9
Elsewhere: RCSB PDB 5CPM · PDBe 5CPM · UniProt Q9R9V9

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