MolNFT v1 · #150183 · protein
[fefe]-hydrogenase cpi from clostridium pasteurianum, variant E282D
6GM2 · Iron hydrogenase 1: “[fefe]-hydrogenase cpi from clostridium pasteurianum, variant E282D”. X-ray diffraction, 4 ligands (SF4, 402, FES), 20 pockets (best druggability 0.80). MolNFT v1 #150183 on GenesisL1: 3D structure, binding…
- PDB
- 6GM2
- Type
- protein
- Length
- 1,150 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
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 578 | 38% helix, 16% strand | P29166 |
| B | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 572 | 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 · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.80 | 0.99 | 28 | 402, SF4 |
| 2 | 109 | 0.80 | 0.99 | 31 | 402, SF4 |
| 3 | 421 | 0.73 | 0.83 | 53 | empty |
| 4 | 397 | 0.65 | 0.79 | 48 | empty |
| 5 | 264 | 0.65 | 0.82 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1520 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 6GM2 · PDBe 6GM2 · UniProt P29166
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