MolNFT v1 · #157782 · protein
Crystal structure of [fefe]-hydrogenase I (cpi) solved with single pulse free electron laser data
6NAC · Iron hydrogenase 1: “Crystal structure of [fefe]-hydrogenase I (cpi) solved with single pulse free electron laser data”. X-ray diffraction, 3 ligands (SF4, 402, FES), 5 pockets (best druggability 0.81). MolNFT v1 #157782 on…
- PDB
- 6NAC
- Type
- protein
- Length
- 573 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
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 573 | 42% 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.81 | 0.99 | 30 | 402, SF4 |
| 2 | 755 | 0.76 | 0.80 | 84 | empty |
| 3 | 110 | 0.43 | 0.77 | 15 | empty |
| 4 | 66 | 0.39 | 0.79 | 14 | empty |
| 5 | 84 | 0.32 | 0.73 | 16 | empty |
Compared structures
- 6NAC · Crystal structure of [FeFe]-hydrogenase I (CpI) solved with single pulse free electron… · 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 6NAC · PDBe 6NAC · UniProt P29166
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