Research workbench
Crystal structure of [nife] hydrogenase from allochromatium vinosum in its ni-a state
Analyse Crystal structure of [nife] hydrogenase from allochromatium vinosum in its ni-a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MYR
- Type
- protein
- Length
- 3,313 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase (nife) small subunit hyda; Nickel-dependent hydrogenase large subunit
- EC
- 1.12.99.6
- UniProt
- D3RV29, D3RV26
- Ligands
- SF4, F3S, NFV, MG, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Hydrogenase (nife) small subunit hyda (EC 1.12.99.6) | protein | 268 | 35% helix, 16% strand | D3RV29 |
| B, H | Nickel-dependent hydrogenase large subunit | protein | 559 | 44% helix, 15% strand | D3RV26 |
| C | Hydrogenase (nife) small subunit hyda (EC 1.12.99.6) | protein | 269 | 35% helix, 16% strand | D3RV29 |
| D, F | Nickel-dependent hydrogenase large subunit | protein | 561 | 45% helix, 15% strand | D3RV26 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- F3S · FE3-S4 cluster · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- NFV · Ni-Fe oxidized active center · ligand · 4 copies · chains B, D, F, H
- MG · Magnesium ion · metal · 4 copies · chains B, D, F, H
- CL · Chloride ion · ion · 4 copies · chains A, C, E, G
- IMD · Imidazole · additive · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.85 | 0.86 | 126 | CL |
| 2 | 1105 | 0.85 | 0.86 | 129 | CL |
| 3 | 1177 | 0.84 | 0.85 | 124 | empty |
| 4 | 132 | 0.80 | 0.97 | 37 | empty |
| 5 | 124 | 0.79 | 0.97 | 35 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3889 Ų buried · 70 hydrogen bonds · protein-protein
- G–H · 3888 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 3884 Ų buried · 70 hydrogen bonds · protein-protein
- E–F · 3872 Ų buried · 72 hydrogen bonds · protein-protein
- A–G · 916 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3MYR · Crystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state · 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 D3RV29
- Every structure of UniProt D3RV26
- Elsewhere: RCSB PDB 3MYR · PDBe 3MYR · UniProt D3RV29 · UniProt D3RV26
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