Research workbench
Crystal structure of oxidoreductase (GFO/IDH/MOCA family member) from porphyromonas gingivalis W83
Analyse Crystal structure of oxidoreductase (GFO/IDH/MOCA family member) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BIO
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, GFO/IDH/MOCA family
- UniProt
- Q7MW40
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase, GFO/IDH/MOCA family | protein | 290 | 38% helix, 32% strand | Q7MW40 |
| B | Oxidoreductase, GFO/IDH/MOCA family | protein | 291 | 38% helix, 32% strand | Q7MW40 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.66 | 0.78 | 34 | EPE, ACT |
| 2 | 496 | 0.66 | 0.78 | 44 | EPE |
| 3 | 55 | 0.40 | 0.81 | 14 | empty |
| 4 | 82 | 0.36 | 0.76 | 16 | empty |
| 5 | 84 | 0.33 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2678 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3BIO · Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas… · 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 Q7MW40
- Elsewhere: RCSB PDB 3BIO · PDBe 3BIO · UniProt Q7MW40
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