Research workbench
Actinobacterial-type nife-hydrogenase from ralstonia eutropha H16 at 2.85 ångström resolution
Analyse Actinobacterial-type nife-hydrogenase from ralstonia eutropha H16 at 2.85… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AA5
- Type
- protein
- Length
- 5,432 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nife-hydrogenase small subunit, hofk; Nife-hydrogenase large subunit, hofg
- EC
- 1.12.99.6
- UniProt
- Q7WXQ4, Q7WXQ3
- Ligands
- SF4, NFU
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, H, M | Nife-hydrogenase small subunit, hofk (EC 1.12.99.6) | protein | 345 | 32% helix, 12% strand | Q7WXQ4 |
| C, G, K | Nife-hydrogenase large subunit, hofg (EC 1.12.99.6) | protein | 561 | 41% helix, 20% strand | Q7WXQ3 |
| E | Nife-hydrogenase large subunit, hofg (EC 1.12.99.6) | protein | 559 | 40% helix, 19% strand | Q7WXQ3 |
| I, L | Nife-hydrogenase large subunit, hofg (EC 1.12.99.6) | protein | 560 | 39% helix, 19% strand | Q7WXQ3 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 18 copies · chains A, C, B, G, D, E, F, L, H, K, M, I
- NFU · formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) · ligand · 6 copies · chains C, E, G, I, K, L
- MLA · Malonic acid · additive · 6 copies · chains H, M, A, F, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.87 | 0.89 | 122 | empty |
| 2 | 806 | 0.87 | 0.91 | 104 | MLA |
| 3 | 1150 | 0.87 | 0.88 | 130 | empty |
| 4 | 636 | 0.81 | 0.86 | 74 | empty |
| 5 | 1093 | 0.73 | 0.76 | 101 | MLA |
Interfaces
27 interfaces between chains.
- B–D · 3287 Ų buried · 55 hydrogen bonds · protein-protein
- D–E · 3219 Ų buried · 46 hydrogen bonds · protein-protein
- A–F · 3215 Ų buried · 57 hydrogen bonds · protein-protein
- H–K · 3181 Ų buried · 47 hydrogen bonds · protein-protein
- H–M · 3160 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 5AA5 · Actinobacterial-type NiFe-hydrogenase from Ralstonia eutropha H16 at 2.85 Angstrom… · 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 Q7WXQ4
- Every structure of UniProt Q7WXQ3
- Elsewhere: RCSB PDB 5AA5 · PDBe 5AA5 · UniProt Q7WXQ4 · UniProt Q7WXQ3
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