MolNFT v1 · #126797 · protein
Crystal structure of an O2-tolerant [nife]-hydrogenase from ralstonia eutropha in its O2-derivatized form by a "soak-and-freeze" derivatization method
5MDL: “Crystal structure of an O2-tolerant [nife]-hydrogenase from ralstonia eutropha in its O2-derivatized form by…”. X-ray diffraction, 8 ligands (NFV, SF4, F3S). MolNFT v1 #126797 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5MDL
- Type
- protein
- Length
- 869 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P31891, P31892
- Ligands
- NFV, SF4, F3S, F4S, MG, OXY, CL, O
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | — | protein | 600 | — | P31891 |
| S | — | protein | 269 | — | 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.
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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