Research workbench
E. COLI hydrogenase-2 (as isolated form).
Analyse E. COLI hydrogenase-2 (as isolated form). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EHQ
- Type
- protein
- Length
- 1,637 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase-2 small chain; Hydrogenase-2 large chain
- EC
- 1.12.99.6
- UniProt
- P69741, P0ACE0
- Ligands
- SF4, F3S, FCO, NI, MG
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Hydrogenase-2 small chain (EC 1.12.99.6) | protein | 267 | 36% helix, 16% strand | P69741 |
| L, M | Hydrogenase-2 large chain (EC 1.12.99.6) | protein | 551 | 46% helix, 17% strand | P0ACE0 |
| T | Hydrogenase-2 small chain (EC 1.12.99.6) | protein | 268 | 35% helix, 16% strand | P69741 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains S, L, T, M
- F3S · FE3-S4 cluster · ligand · 2 copies · chains S, L, T, M
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains L, M
- NI · Nickel (II) ion · metal · 2 copies · chains L, M
- MG · Magnesium ion · metal · 2 copies · chains L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.83 | 0.97 | 53 | empty |
| 2 | 1028 | 0.83 | 0.84 | 84 | empty |
| 3 | 76 | 0.73 | 0.96 | 22 | empty |
| 4 | 79 | 0.73 | 0.96 | 23 | empty |
| 5 | 52 | 0.60 | 0.91 | 18 | empty |
Interfaces
6 interfaces between chains.
- T–M · 3793 Ų buried · 56 hydrogen bonds · protein-protein
- S–L · 3767 Ų buried · 54 hydrogen bonds · protein-protein
- S–M · 784 Ų buried · 6 hydrogen bonds · protein-protein
- L–T · 774 Ų buried · 6 hydrogen bonds · protein-protein
- S–T · 753 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6EHQ · E. coli Hydrogenase-2 (as isolated form). · the same entry in another collection · chain S against S, TM-score 1.00
- P0ACE0 · AlphaFold monomer V2.0 prediction for hydrogenase-2 large chain (P0ACE0) · a predicted model of the same protein · chain L against A, TM-score 1.00
- P69741 · AlphaFold monomer V2.0 prediction for hydrogenase-2 small chain (P69741) · 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 P69741
- Every structure of UniProt P0ACE0
- Elsewhere: RCSB PDB 6EHQ · PDBe 6EHQ · UniProt P69741 · UniProt P0ACE0
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