Research workbench
The crystal structure of [fe]-hydrogenase holoenzyme (hmd) from methanocaldococcus jannaschii
Analyse The crystal structure of [fe]-hydrogenase holoenzyme (hmd) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DAG
- 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
- Q58194
- Ligands
- FEG, FE2, CMO
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5,10-methenyltetrahydromethanopterin hydrogenase (EC 1.12.98.2) | protein | 344 | 54% helix, 13% strand | Q58194 |
Ligands and binding sites
- FEG · 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine · ligand · chains A
- FE2 · Fe (II) ion · metal · chains A
- CMO · Carbon monoxide · ion · 2 copies · 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 | 586 | 0.66 | 0.76 | 30 | empty |
| 2 | 280 | 0.58 | 0.77 | 36 | FE2, FEG, CMO |
Compared structures
- 3DAG · The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58194 · AlphaFold monomer V2.0 prediction for 5,10-methenyltetrahydromethanopterin hydrogenase… · a predicted model of the same protein · chain A against A, TM-score 0.86
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 Q58194
- Elsewhere: RCSB PDB 3DAG · PDBe 3DAG · UniProt Q58194
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