Research workbench
Structure of putative oxidoreductase (TM_0425) from thermotoga maritima
Analyse Structure of putative oxidoreductase (TM_0425) from thermotoga maritima in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IP3
- Type
- protein
- Length
- 2,631 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, putative
- UniProt
- Q9WYQ6
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Oxidoreductase, putative | protein | 328 | 37% helix, 26% strand | Q9WYQ6 |
| B | Oxidoreductase, putative | protein | 331 | 36% helix, 26% strand | Q9WYQ6 |
| C, F | Oxidoreductase, putative | protein | 330 | 36% helix, 26% strand | Q9WYQ6 |
| G | Oxidoreductase, putative | protein | 327 | 37% helix, 26% strand | Q9WYQ6 |
| H | Oxidoreductase, putative | protein | 329 | 37% helix, 26% strand | Q9WYQ6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.83 | 0.87 | 93 | empty |
| 2 | 518 | 0.81 | 0.88 | 71 | empty |
| 3 | 130 | 0.80 | 0.98 | 23 | empty |
| 4 | 128 | 0.80 | 0.98 | 24 | empty |
| 5 | 137 | 0.80 | 0.97 | 26 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1917 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1914 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1909 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1886 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 547 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 3IP3 · Structure of putative oxidoreductase (TM_0425) from Thermotoga maritima · 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 Q9WYQ6
- Elsewhere: RCSB PDB 3IP3 · PDBe 3IP3 · UniProt Q9WYQ6
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