MolNFT v1 · #29714 · protein
Crystal structure of oxidoreductase (TM0312) from thermotoga maritima at 2.50 a resolution
1ZH8: “Crystal structure of oxidoreductase (TM0312) from thermotoga maritima at 2.50 a resolution”. X-ray diffraction, 2 ligands (NAP, NA), 3 pockets (best druggability 0.69). MolNFT v1 #29714 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1ZH8
- Type
- protein
- Length
- 649 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase
- EC
- 1.1.1.-
- UniProt
- Q9WYE8
- Ligands
- NAP, NA
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase (EC 1.1.1.-) | protein | 325 | 40% helix, 26% strand | Q9WYE8 |
| B | Oxidoreductase (EC 1.1.1.-) | protein | 324 | 39% helix, 26% strand | Q9WYE8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.69 | 0.77 | 62 | NAP, EDO |
| 2 | 563 | 0.68 | 0.78 | 62 | NAP |
| 3 | 69 | 0.40 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1190 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1ZH8 · Crystal structure of Oxidoreductase (TM0312) from Thermotoga maritima at 2.50 A resolution · 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 Q9WYE8
- Elsewhere: RCSB PDB 1ZH8 · PDBe 1ZH8 · UniProt Q9WYE8
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