MolNFT v1 · #115639 · protein
Crystal structure of xena from pseudomonas putida in complex with an NADH mimic (mbu)
5CPO · Xenobiotic reductase: “Crystal structure of xena from pseudomonas putida in complex with an NADH mimic (mbu)”. X-ray diffraction, 3 ligands (XEN, FNR, CA), 3 pockets (best druggability 0.77). MolNFT v1 #115639 on GenesisL1: 3D…
- PDB
- 5CPO
- 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
- XEN, FNR, CA
- Pockets
- 3 · best druggability 0.77
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
- XEN · 1-butyl-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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.77 | 0.83 | 51 | XEN, FNR |
| 2 | 802 | 0.76 | 0.80 | 73 | XEN, FNR |
| 3 | 80 | 0.32 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1357 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5CPO · Crystal structure of XenA from Pseudomonas putida in complex with an NADH mimic (mBu) · 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 5CPO · PDBe 5CPO · UniProt Q9R9V9
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