Research workbench
Binding of exogenously added carbon monoxide at the active site of the fe-only hydrogenase (cpi) from clostridium pasteurianum
Analyse Binding of exogenously added carbon monoxide at the active site of the fe-only… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C4A
- Type
- protein
- Length
- 574 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (fe-only hydrogenase)
- EC
- 1.18.99.1
- UniProt
- P29166
- Ligands
- SF4, HC1, FES
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (fe-only hydrogenase) (EC 1.18.99.1) | protein | 574 | 40% helix, 17% strand | P29166 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A
- HC1 · 2 iron/2 sulfur/5 carbonyl/2 water inorganic cluster · ligand · chains A
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.80 | 0.99 | 29 | HC1, SF4 |
| 2 | 785 | 0.75 | 0.80 | 83 | empty |
| 3 | 110 | 0.55 | 0.83 | 22 | SF4 |
| 4 | 83 | 0.40 | 0.77 | 13 | empty |
| 5 | 66 | 0.36 | 0.78 | 19 | empty |
Compared structures
- 1C4A · Binding of exogenously added carbon monoxide at the active site of the fe-only… · the same entry in another collection · chain A against A, TM-score 1.00
- P29166 · AlphaFold monomer V2.0 prediction for iron hydrogenase 1 (P29166) · a predicted model of the same protein · chain A 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 P29166
- Elsewhere: RCSB PDB 1C4A · PDBe 1C4A · UniProt P29166
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