Research workbench
Crystal structure of oxidoreductase domain protein from kribbella flavida
Analyse Crystal structure of oxidoreductase domain protein from kribbella flavida in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H3V
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase domain protein
- UniProt
- D2PU28
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase domain protein | protein | 385 | 38% helix, 25% strand | D2PU28 |
| B | Oxidoreductase domain protein | protein | 375 | 38% helix, 26% strand | D2PU28 |
Ligands and binding sites
- FMT · Formic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.64 | 0.85 | 31 | empty |
| 2 | 203 | 0.63 | 0.83 | 30 | empty |
| 3 | 287 | 0.62 | 0.80 | 23 | empty |
| 4 | 91 | 0.37 | 0.75 | 16 | FMT |
| 5 | 93 | 0.34 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1837 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 4H3V · Crystal structure of oxidoreductase domain protein from Kribbella flavida · 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 D2PU28
- Elsewhere: RCSB PDB 4H3V · PDBe 4H3V · UniProt D2PU28
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