MolNFT v1 · #157620 · protein
1.0 ångström crystal structure of [fefe]-hydrogenase
6N59 · Iron hydrogenase 1: “1.0 ångström crystal structure of [fefe]-hydrogenase”. X-ray diffraction, 3 ligands (SF4, 402, FES), 7 pockets (best druggability 0.80). MolNFT v1 #157620 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6N59
- Type
- protein
- Length
- 570 residues
- Chains
- 1
- 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
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 570 | 43% helix, 16% strand | P29166 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A
- 402 · dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) · ligand · chains A
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.80 | 0.99 | 31 | 402, SF4 |
| 2 | 718 | 0.75 | 0.80 | 93 | GOL |
| 3 | 89 | 0.41 | 0.78 | 14 | empty |
| 4 | 65 | 0.35 | 0.77 | 17 | empty |
| 5 | 55 | 0.33 | 0.77 | 17 | empty |
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 6N59 · PDBe 6N59 · UniProt P29166
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