Research workbench
TmHydABC- T. maritima bifurcating hydrogenase with bridge domain closed
Analyse TmHydABC- T. maritima bifurcating hydrogenase with bridge domain closed in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P91
- Type
- protein
- Length
- 2,681 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 /…
- Molecule
- Fe-hydrogenase, subunit alpha; Fe-hydrogenase, subunit beta; Fe-hydrogenase, subunit gamma
- EC
- 1.12.1.4
- UniProt
- G4FFG1, G4FFG0, Q9S5X7
- Ligands
- SF4, FES, FMN, ZN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · resolution 2.8 · 5 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Fe-hydrogenase, subunit alpha (EC 1.12.1.4) | protein | 642 | 39% helix, 16% strand | G4FFG1 |
| b | Fe-hydrogenase, subunit beta (EC 1.12.1.4) | protein | 560 | 45% helix, 13% strand | G4FFG0 |
| c, C | Fe-hydrogenase, subunit gamma (EC 1.12.1.4) | protein | 156 | 51% helix, 12% strand | Q9S5X7 |
| A | Fe-hydrogenase, subunit alpha (EC 1.12.1.4) | protein | 554 | 41% helix, 17% strand | G4FFG1 |
| B | Fe-hydrogenase, subunit beta (EC 1.12.1.4) | protein | 613 | 43% helix, 13% strand | G4FFG0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 12 copies · chains a, A, b, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 7 copies · chains a, b, c, A, B, C
- FMN · Flavin mononucleotide · ligand · 2 copies · chains b, B
- ZN · Zinc ion · metal · 2 copies · chains b, B
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 | 102 | 0.80 | 0.99 | 29 | SF4 |
| 2 | 953 | 0.79 | 0.81 | 110 | empty |
| 3 | 725 | 0.78 | 0.82 | 77 | empty |
| 4 | 83 | 0.77 | 0.99 | 26 | SF4 |
| 5 | 621 | 0.73 | 0.80 | 63 | FMN |
Interfaces
10 interfaces between chains.
- a–A · 2557 Ų buried · 33 hydrogen bonds · protein-protein
- a–c · 1641 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1505 Ų buried · 11 hydrogen bonds · protein-protein
- b–c · 1458 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1325 Ų buried · 12 hydrogen bonds · protein-protein
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 G4FFG1
- Every structure of UniProt G4FFG0
- Every structure of UniProt Q9S5X7
- Elsewhere: RCSB PDB 7P91 · PDBe 7P91 · UniProt G4FFG1 · UniProt G4FFG0 · UniProt Q9S5X7
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