Research workbench
Co-dependent transcription factor cooa from carboxydothermus hydrogenoformans (imidazole-bound form)
Analyse Co-dependent transcription factor cooa from carboxydothermus hydrogenoformans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FMY
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon monoxide oxidation system transcription regulator cooa-1
- Ligands
- HEM
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Carbon monoxide oxidation system transcription regulator cooa-1 | protein | 218 | 42% helix, 27% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.74 | 0.80 | 60 | HEM, IMD |
| 2 | 662 | 0.73 | 0.79 | 54 | HEM, IMD |
| 3 | 245 | 0.73 | 0.87 | 31 | HEM, IMD |
| 4 | 558 | 0.72 | 0.80 | 63 | empty |
| 5 | 249 | 0.71 | 0.85 | 31 | HEM, IMD |
Interfaces
3 interfaces between chains.
- C–D · 1646 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1548 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2FMY · CO-dependent transcription factor CooA from Carboxydothermus hydrogenoformans… · 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
- Elsewhere: RCSB PDB 2FMY · PDBe 2FMY
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