Research workbench
[fefe]-hydrogenase cpi from clostridium pasteurianum, variant R286A
Analyse [fefe]-hydrogenase cpi from clostridium pasteurianum, variant R286A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GM3
- Type
- protein
- Length
- 1,149 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron hydrogenase 1
- EC
- 1.12.7.2
- UniProt
- P29166
- Ligands
- SF4, 402, FES, MG
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 574 | 41% helix, 17% strand | P29166 |
| B | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 575 | 40% helix, 16% strand | P29166 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B
- 402 · dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) · ligand · 2 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.80 | 0.99 | 31 | 402, SF4 |
| 2 | 109 | 0.80 | 0.99 | 32 | 402, SF4 |
| 3 | 856 | 0.77 | 0.81 | 94 | empty |
| 4 | 459 | 0.69 | 0.80 | 64 | MG |
| 5 | 326 | 0.68 | 0.82 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 1530 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
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 6GM3 · PDBe 6GM3 · UniProt P29166
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