MolNFT v1 · #70859 · protein
Stepwise [fefe]-hydrogenase H-cluster assembly revealed in the structure of HYDA(DELTAEFG)
3LX4 · Fe-hydrogenase: “Stepwise [fefe]-hydrogenase H-cluster assembly revealed in the structure of HYDA(DELTAEFG)”. X-ray diffraction, 2 ligands (SF4, CL), 10 pockets (best druggability 0.84). MolNFT v1 #70859 on GenesisL1: 3D structure…
- PDB
- 3LX4
- Type
- protein
- Length
- 814 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fe-hydrogenase
- EC
- 1.18.99.1
- UniProt
- Q9FYU1
- Ligands
- SF4, CL
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fe-hydrogenase (EC 1.18.99.1) | protein | 407 | 44% helix, 14% strand | Q9FYU1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.84 | 0.85 | 101 | SF4, CL, ACT |
| 2 | 658 | 0.79 | 0.84 | 53 | SF4, CL, ACT |
| 3 | 234 | 0.65 | 0.83 | 28 | empty |
| 4 | 83 | 0.56 | 0.87 | 26 | empty |
| 5 | 165 | 0.55 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 801 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3LX4 · Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9FYU1
- Elsewhere: RCSB PDB 3LX4 · PDBe 3LX4 · UniProt Q9FYU1
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