Research workbench
Structure of fully reduced hydrogenase (hyd-1) variant E28Q
Analyse Structure of fully reduced hydrogenase (hyd-1) variant E28Q in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FPI
- Type
- protein
- Length
- 1,698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase-1 small chain; Hydrogenase-1 large chain
- EC
- 1.12.99.6
- UniProt
- P69739, P0ACD8
- Ligands
- SF4, F3S, SF3, EJ2, MG, CL, SO4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S, T | Hydrogenase-1 small chain (EC 1.12.99.6) | protein | 268 | 35% helix, 18% strand | P69739 |
| L, M | Hydrogenase-1 large chain (EC 1.12.99.6) | protein | 581 | 43% helix, 16% strand | P0ACD8 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains S, T
- F3S · FE3-S4 cluster · ligand · 2 copies · chains S, L, T, M
- SF3 · FE4-S3 cluster · ligand · 2 copies · chains S, L, T, M
- EJ2 · Ni-Fe reduced active center · ligand · 2 copies · chains L, M
- MG · Magnesium ion · metal · 2 copies · chains L, M
- CL · Chloride ion · ion · 6 copies · chains S, T
- SO4 · Sulfate ion · ion · chains S, L
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.82 | 0.83 | 119 | empty |
| 2 | 95 | 0.63 | 0.88 | 20 | LMT |
| 3 | 93 | 0.60 | 0.86 | 19 | LMT |
| 4 | 179 | 0.50 | 0.77 | 35 | empty |
| 5 | 161 | 0.50 | 0.78 | 34 | empty |
Interfaces
6 interfaces between chains.
- T–M · 4033 Ų buried · 63 hydrogen bonds · protein-protein
- S–L · 4007 Ų buried · 69 hydrogen bonds · protein-protein
- S–M · 842 Ų buried · 8 hydrogen bonds · protein-protein
- L–T · 841 Ų buried · 8 hydrogen bonds · protein-protein
- S–T · 659 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6FPI · Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q · the same entry in another collection · chain S against S, TM-score 1.00
- P0ACD8 · AlphaFold monomer V2.0 prediction for hydrogenase-1 large chain (P0ACD8) · a predicted model of the same protein · chain L against A, TM-score 1.00
- P69739 · AlphaFold monomer V2.0 prediction for hydrogenase-1 small chain (P69739) · a predicted model of the same protein · chain S 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 P69739
- Every structure of UniProt P0ACD8
- Elsewhere: RCSB PDB 6FPI · PDBe 6FPI · UniProt P69739 · UniProt P0ACD8
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