MolNFT v1 · #140203 · protein
Membrane-bound respiratory [nife]-hydrogenase from hydrogenovibrio marinus in a ferricyanide-oxidized condition
5Y34: “Membrane-bound respiratory [nife]-hydrogenase from hydrogenovibrio marinus in a ferricyanide-oxidized…”. X-ray diffraction, 7 ligands (FCO, SF3, F3S), 12 pockets (best druggability 0.82). MolNFT v1 #140203 on GenesisL1: 3D…
- PDB
- 5Y34
- Type
- protein
- Length
- 1,730 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase; Membrane-bound hydrogenase small subunit
- EC
- 1.12.5.1
- UniProt
- F2Z6J6, F2Z6J5
- Ligands
- FCO, SF3, F3S, SF4, 3NI, MG, O
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hydrogenase (EC 1.12.5.1) | protein | 595 | 44% helix, 16% strand | F2Z6J6 |
| B | Membrane-bound hydrogenase small subunit | protein | 273 | 36% helix, 17% strand | F2Z6J5 |
| D | Membrane-bound hydrogenase small subunit | protein | 267 | 36% helix, 17% strand | F2Z6J5 |
Ligands and binding sites
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains A, C
- SF3 · FE4-S3 cluster · ligand · 2 copies · chains A, B, C, D
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B, C, D
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, D
- 3NI · Nickel (III) ion · metal · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- O · Oxygen atom · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.82 | 0.96 | 47 | empty |
| 2 | 151 | 0.82 | 0.97 | 40 | empty |
| 3 | 889 | 0.77 | 0.80 | 81 | empty |
| 4 | 63 | 0.71 | 0.98 | 25 | empty |
| 5 | 295 | 0.70 | 0.84 | 32 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3977 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3968 Ų buried · 68 hydrogen bonds · protein-protein
- B–C · 886 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 881 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 586 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5Y34 · Membrane-bound respiratory [NiFe]-hydrogenase from Hydrogenovibrio marinus in a… · 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 F2Z6J6
- Every structure of UniProt F2Z6J5
- Elsewhere: RCSB PDB 5Y34 · PDBe 5Y34 · UniProt F2Z6J6 · UniProt F2Z6J5
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