MolNFT v1 · #129429 · protein
Crystal structure of native [fe]-hydrogenase hmd from methanothermobacter marburgensis inactivated by O2.
5OK4 · 5,10-methenyltetrahydromethanopterin hydrogenase: “Crystal structure of native [fe]-hydrogenase hmd from methanothermobacter marburgensis inactivated by O2.”. X-ray diffraction, 2 ligands (FEG, FE), 2 pockets (best druggability…
- PDB
- 5OK4
- Type
- protein
- Length
- 344 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5,10-methenyltetrahydromethanopterin hydrogenase
- EC
- 1.12.98.2
- UniProt
- P32440
- Ligands
- FEG, FE
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5,10-methenyltetrahydromethanopterin hydrogenase (EC 1.12.98.2) | protein | 344 | 55% helix, 12% strand | P32440 |
Ligands and binding sites
- FEG · 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine · ligand · chains A
- FE · Fe (III) ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.66 | 0.75 | 36 | empty |
| 2 | 330 | 0.60 | 0.78 | 50 | FE, FEG |
Compared structures
- 5OK4 · Crystal structure of native [Fe]-hydrogenase Hmd from Methanothermobacter marburgensis… · the same entry in another collection · chain A against A, TM-score 1.00
- P32440 · AlphaFold monomer V2.0 prediction for 5,10-methenyltetrahydromethanopterin hydrogenase… · a predicted model of the same protein · chain A against A, TM-score 0.80
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 P32440
- Elsewhere: RCSB PDB 5OK4 · PDBe 5OK4 · UniProt P32440
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