Research workbench
Crystal structure of the O2-tolerant mbh-P242C from ralstonia eutropha in its reduced state
Analyse Crystal structure of the O2-tolerant mbh-P242C from ralstonia eutropha in its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ODG
- Type
- protein
- Length
- 868 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uptake hydrogenase large subunit; Uptake hydrogenase small subunit
- EC
- 1.12.99.6
- UniProt
- P31891, P31892
- Ligands
- SF4, NFU, F4S, MG, CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Uptake hydrogenase large subunit (EC 1.12.99.6) | protein | 598 | 44% helix, 16% strand | P31891 |
| S | Uptake hydrogenase small subunit (EC 1.12.99.6) | protein | 270 | 35% helix, 16% strand | P31892 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains S, L
- NFU · formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) · ligand · chains L
- F4S · FE4-S3 cluster · ligand · chains L, S
- MG · Magnesium ion · metal · chains L
- CL · Chloride ion · ion · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.81 | 0.94 | 47 | empty |
| 2 | 306 | 0.67 | 0.82 | 28 | empty |
| 3 | 131 | 0.40 | 0.75 | 20 | empty |
| 4 | 52 | 0.36 | 0.79 | 19 | empty |
| 5 | 70 | 0.35 | 0.76 | 21 | CL |
Interfaces
1 interface between chains.
- L–S · 3970 Ų buried · 66 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 7ODG · Crystal structure of the O2-tolerant MBH-P242C from Ralstonia eutropha in its reduced… · the same entry in another collection · chain L against L, TM-score 1.00
- P31891 · AlphaFold monomer V2.0 prediction for uptake hydrogenase large subunit (P31891) · a predicted model of the same protein · chain L against A, TM-score 1.00
- P31892 · AlphaFold monomer V2.0 prediction for uptake hydrogenase small subunit (P31892) · a predicted model of the same protein · chain S against A, TM-score 0.99
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 P31891
- Every structure of UniProt P31892
- Elsewhere: RCSB PDB 7ODG · PDBe 7ODG · UniProt P31891 · UniProt P31892
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