Research workbench
Structure of E. COLI hydrogenase-1 C19G variant in complex with cytochrome B
Analyse Structure of E. COLI hydrogenase-1 C19G variant in complex with cytochrome B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G94
- Type
- protein
- Length
- 3,834 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase-1 small chain; Hydrogenase-1 large chain; Probable NI/FE-hydrogenase 1 B-type…
- EC
- 1.12.99.6
- UniProt
- P69739, P0ACD8, P0AAM1
- Ligands
- SF4, F3S, ER2, FCO, HEM, NI, MG, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Hydrogenase-1 small chain (EC 1.12.99.6) | protein | 296 | 38% helix, 17% strand | P69739 |
| L, M, J, K | Hydrogenase-1 large chain (EC 1.12.99.6) | protein | 581 | 43% helix, 16% strand | P0ACD8 |
| T | Hydrogenase-1 small chain (EC 1.12.99.6) | protein | 296 | 40% helix, 17% strand | P69739 |
| Q | Hydrogenase-1 small chain (EC 1.12.99.6) | protein | 295 | 38% helix, 17% strand | P69739 |
| R | Hydrogenase-1 small chain (EC 1.12.99.6) | protein | 291 | 39% helix, 18% strand | P69739 |
| A | Probable NI/FE-hydrogenase 1 B-type cytochrome subunit | protein | 172 | 70% helix, 0% strand | P0AAM1 |
| B | Probable NI/FE-hydrogenase 1 B-type cytochrome subunit | protein | 160 | 69% helix, 0% strand | P0AAM1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains S, T, Q, R
- F3S · FE3-S4 cluster · ligand · 4 copies · chains S, L, T, M, Q, J, R, K
- ER2 · Fe4S4 · ligand · 4 copies · chains S, L, T, M, Q, J, R, K
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 4 copies · chains L, M, J, K
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 4 copies · chains L, M, J, K
- MG · Magnesium ion · metal · 4 copies · chains L, M, J, K
- CL · Chloride ion · ion · 4 copies · chains L, M, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.86 | 0.87 | 99 | empty |
| 2 | 488 | 0.84 | 0.91 | 66 | HEM |
| 3 | 664 | 0.84 | 0.88 | 81 | HEM |
| 4 | 1140 | 0.82 | 0.83 | 119 | CL |
| 5 | 1167 | 0.81 | 0.82 | 93 | CL |
Interfaces
26 interfaces between chains.
- R–K · 4148 Ų buried · 70 hydrogen bonds · protein-protein
- S–L · 4051 Ų buried · 68 hydrogen bonds · protein-protein
- T–M · 4034 Ų buried · 64 hydrogen bonds · protein-protein
- Q–J · 4011 Ų buried · 66 hydrogen bonds · protein-protein
- T–A · 1937 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6G94 · Structure of E. coli hydrogenase-1 C19G variant in complex with cytochrome b · the same entry in another collection · chain B against B, 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 Q against A, TM-score 0.99
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
- Every structure of UniProt P0AAM1
- Elsewhere: RCSB PDB 6G94 · PDBe 6G94 · UniProt P69739 · UniProt P0ACD8 · UniProt P0AAM1
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