Research workbench
Crystal structure of xena from pseudomonas putida in complex with an NADH mimic (mbu)
Analyse Crystal structure of xena from pseudomonas putida in complex with an NADH mimic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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