Research workbench
Crystal structure of an O2-tolerant [nife]-hydrogenase from ralstonia eutropha in its O2-derivatized form by a "soak-and-freeze" derivatization method
Analyse Crystal structure of an O2-tolerant [nife]-hydrogenase from ralstonia eutropha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MDL
- Type
- protein
- Length
- 869 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
- NFV, SF4, F3S, F4S, MG, OXY, CL, O
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Uptake hydrogenase large subunit (EC 1.12.99.6) | protein | 600 | 44% helix, 16% strand | P31891 |
| S | Uptake hydrogenase small subunit (EC 1.12.99.6) | protein | 269 | 36% helix, 17% strand | P31892 |
Ligands and binding sites
- NFV · Ni-Fe oxidized active center · ligand · chains L
- SF4 · Iron/sulfur cluster · ligand · chains S
- F3S · FE3-S4 cluster · ligand · chains L, S
- F4S · FE4-S3 cluster · ligand · chains L, S
- MG · Magnesium ion · metal · chains L
- OXY · Oxygen molecule · ion · 4 copies · chains L, S
- CL · Chloride ion · ion · chains S
- O · Oxygen atom · ion · chains L, S
- PEG · Di(hydroxyethyl)ether · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.81 | 0.96 | 44 | OXY |
| 2 | 275 | 0.67 | 0.83 | 27 | empty |
| 3 | 172 | 0.47 | 0.76 | 21 | empty |
| 4 | 85 | 0.40 | 0.77 | 23 | empty |
| 5 | 59 | 0.33 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- L–S · 4002 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 5MDL · Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its… · 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 5MDL · PDBe 5MDL · UniProt P31891 · UniProt P31892
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