Research workbench
The carbon monoxide complex of [nife]-hydrogenase (hyb-type) from citrobacter sp. S-77
Analyse The carbon monoxide complex of [nife]-hydrogenase (hyb-type) from citrobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VXQ
- Type
- protein
- Length
- 1,638 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [nife]-hydrogenase 2 large subunit; Nife hydrogenase
- EC
- 1.12.99.6
- UniProt
- A0A3B6UEQ1, A0A3B6UEQ0
- Ligands
- SF4, NFU, F3S, MG, CMO
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | [nife]-hydrogenase 2 large subunit | protein | 551 | 44% helix, 18% strand | A0A3B6UEQ1 |
| B, D | Nife hydrogenase (EC 1.12.99.6) | protein | 268 | 37% helix, 15% strand | A0A3B6UEQ0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains B, A, D, C
- NFU · formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) · ligand · 2 copies · chains A, C
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
- CMO · Carbon monoxide · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.81 | 0.84 | 60 | empty |
| 2 | 97 | 0.76 | 0.97 | 27 | empty |
| 3 | 91 | 0.76 | 0.98 | 29 | empty |
| 4 | 91 | 0.76 | 0.96 | 22 | empty |
| 5 | 69 | 0.72 | 0.96 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3753 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 3737 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 779 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 765 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 749 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7VXQ · The Carbon Monoxide Complex of [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 · 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 A0A3B6UEQ1
- Every structure of UniProt A0A3B6UEQ0
- Elsewhere: RCSB PDB 7VXQ · PDBe 7VXQ · UniProt A0A3B6UEQ1 · UniProt A0A3B6UEQ0
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