Research workbench
Structure of fully reduced hydrogenase (hyd-1) variant E28Q collected at pH 10
Analyse Structure of fully reduced hydrogenase (hyd-1) variant E28Q collected at pH 10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GAL
- Type
- protein
- Length
- 1,692 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, LI, CL, SO4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Hydrogenase-1 small chain (EC 1.12.99.6) | protein | 264 | 35% helix, 19% strand | P69739 |
| L, M | Hydrogenase-1 large chain (EC 1.12.99.6) | protein | 581 | 44% helix, 17% strand | P0ACD8 |
| T | Hydrogenase-1 small chain (EC 1.12.99.6) | protein | 266 | 36% helix, 18% strand | P69739 |
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
- LI · Lithium ion · metal · 2 copies · chains T, M
- CL · Chloride ion · ion · 2 copies · chains S, T
- SO4 · Sulfate ion · ion · 2 copies · chains S, T, M
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains M
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 | 1136 | 0.80 | 0.81 | 93 | empty |
| 2 | 59 | 0.71 | 0.98 | 19 | empty |
| 3 | 51 | 0.70 | 0.98 | 19 | empty |
| 4 | 69 | 0.68 | 0.95 | 35 | empty |
| 5 | 77 | 0.60 | 0.88 | 19 | empty |
Interfaces
6 interfaces between chains.
- T–M · 4133 Ų buried · 72 hydrogen bonds · protein-protein
- S–L · 4022 Ų buried · 71 hydrogen bonds · protein-protein
- S–M · 850 Ų buried · 8 hydrogen bonds · protein-protein
- L–T · 831 Ų buried · 9 hydrogen bonds · protein-protein
- S–T · 689 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6GAL · Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q collected at pH 10 · 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 6GAL · PDBe 6GAL · UniProt P69739 · UniProt P0ACD8
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