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The crystal structure of C176A mutated [fe]-hydrogenase (hmd) holoenzyme from methanocaldococcus jannaschii
Analyse The crystal structure of C176A mutated [fe]-hydrogenase (hmd) holoenzyme from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F46
- Type
- protein
- Length
- 345 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
- I2C, DTV, FE2, CMO
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5,10-methenyltetrahydromethanopterin hydrogenase (EC 1.12.98.2) | protein | 345 | 53% helix, 12% strand | Q58194 |
Ligands and binding sites
- I2C · 5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine · ligand · chains A
- DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · 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 | 609 | 0.67 | 0.76 | 31 | empty |
| 2 | 301 | 0.58 | 0.77 | 31 | I2C, FE2, CMO, DTV |
Compared structures
- 3F46 · The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme from… · 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 3F46 · PDBe 3F46 · UniProt Q58194
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