MolNFT v1 · #109798 · protein
Apo [fefe]-hydrogenase cpi
4XDD · Iron hydrogenase 1: “Apo [fefe]-hydrogenase cpi”. X-ray diffraction, 4 ligands (SF4, FES, MG), 17 pockets (best druggability 0.80). MolNFT v1 #109798 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XDD
- Type
- protein
- Length
- 1,163 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, FES, MG, CL
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 582 | 43% helix, 16% strand | P29166 |
| B | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 581 | 42% helix, 17% strand | P29166 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.80 | 0.99 | 30 | SF4, CL |
| 2 | 101 | 0.79 | 0.99 | 27 | SF4, CL |
| 3 | 513 | 0.74 | 0.82 | 75 | MG |
| 4 | 233 | 0.66 | 0.84 | 41 | empty |
| 5 | 407 | 0.65 | 0.78 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 1577 Ų buried · 14 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 4XDD · PDBe 4XDD · UniProt P29166
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