MolNFT v1 · #25357 · protein
Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from thermotoga maritima at 2.40 a resolution
1VP5: “Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from thermotoga maritima at 2.40 a…”. X-ray diffraction, 1 ligand (NAP), 3 pockets (best druggability 0.67). MolNFT v1 #25357 on GenesisL1: 3D structure, binding…
- PDB
- 1VP5
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,5-diketo-D-gluconic acid reductase
- EC
- 1.1.1.274
- UniProt
- Q9X0A2
- Ligands
- NAP
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,5-diketo-D-gluconic acid reductase (EC 1.1.1.274) | protein | 284 | 49% helix, 16% strand | Q9X0A2 |
| B | 2,5-diketo-D-gluconic acid reductase (EC 1.1.1.274) | protein | 283 | 48% helix, 16% strand | Q9X0A2 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.67 | 0.81 | 39 | NAP |
| 2 | 321 | 0.66 | 0.81 | 42 | NAP |
| 3 | 527 | 0.64 | 0.76 | 62 | empty |
Interfaces
1 interface between chains.
- A–B · 270 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1VP5 · Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from Thermotoga… · 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 Q9X0A2
- Elsewhere: RCSB PDB 1VP5 · PDBe 1VP5 · UniProt Q9X0A2
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