Research workbench
Cryo-EM structure of hydrogen-dependent CO2 reductase.
Analyse Cryo-EM structure of hydrogen-dependent CO2 reductase. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QV7
- Type
- protein
- Length
- 5,276 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogen dependent carbon dioxide reductase subunit HYCB3; Hydrogen dependent carbon…
- EC
- 1.-.-.-, 1.12.7.2, 1.2.1.2
- UniProt
- A0A097ATJ9, A0A097ATK6, A0A097ATH7, A0A097ATK5
- Ligands
- SF4, 402
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 32% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Hydrogen dependent carbon dioxide reductase subunit HYCB3 (EC 1.-.-.-) | protein | 174 | 30% helix, 15% strand | A0A097ATJ9 |
| B, C, J, N, P, X | Hydrogen dependent carbon dioxide reductase subunit HYCB4 (EC 1.-.-.-) | protein | 183 | 22% helix, 19% strand | A0A097ATK6 |
| D, K, Q, R, V, Z | Hydrogen dependent carbon dioxide reductase subunit HYDA2 (EC 1.12.7.2) | protein | 448 | 34% helix, 12% strand | A0A097ATH7 |
| S, Y | Hydrogen dependent carbon dioxide reductase subunit fdhf (EC 1.2.1.2) | protein | 571 | 33% helix, 14% strand | A0A097ATK5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 52 copies · chains A, B, C, D, G, J, K, N, P, Q, R, S, V, X, Y, Z
- 402 · dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) · ligand · 6 copies · chains D, K, Q, R, V, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.84 | 0.96 | 50 | SF4, 402 |
| 2 | 246 | 0.83 | 0.95 | 49 | 402, SF4 |
| 3 | 177 | 0.82 | 0.97 | 44 | 402, SF4 |
| 4 | 120 | 0.80 | 0.98 | 30 | 402, SF4 |
| 5 | 126 | 0.80 | 0.98 | 26 | 402, SF4 |
Interfaces
31 interfaces between chains.
- B–N · 1615 Ų buried · 7 hydrogen bonds · protein-protein
- G–X · 1598 Ų buried · 13 hydrogen bonds · protein-protein
- A–P · 1575 Ų buried · 13 hydrogen bonds · protein-protein
- C–X · 1559 Ų buried · 13 hydrogen bonds · protein-protein
- J–P · 1548 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent, 5 disulfide (covalent ligand, disulfide).
Compared structures
- 7QV7 · Cryo-EM structure of Hydrogen-dependent CO2 reductase. · the same entry in another collection · chain A 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 A0A097ATJ9
- Every structure of UniProt A0A097ATK6
- Every structure of UniProt A0A097ATH7
- Every structure of UniProt A0A097ATK5
- Elsewhere: RCSB PDB 7QV7 · PDBe 7QV7 · UniProt A0A097ATJ9 · UniProt A0A097ATK6 · UniProt A0A097ATH7 · UniProt A0A097ATK5
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