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Crystal structure of a truncated form of Thermus thermophilus CarH bound to adenosylcobalamin (dark state)
Analyse Crystal structure of a truncated form of Thermus thermophilus CarH bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C8A
- Type
- protein
- Length
- 777 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Thermus thermophilus
- Molecule
- Light-dependent transcriptional regulator CarH
- UniProt
- Q746J7
- Ligands
- B12, 5AD
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.15 · 3 distinct chains · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Light-dependent transcriptional regulator CarH | protein | 194 | 56% helix, 10% strand | Q746J7 |
| B | Light-dependent transcriptional regulator CarH | protein | 194 | 55% helix, 10% strand | Q746J7 |
| C | Light-dependent transcriptional regulator CarH | protein | 195 | 55% helix, 10% strand | Q746J7 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 4 copies · chains A, B, C, D
- 5AD · 5'-deoxyadenosine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.84 | 0.91 | 92 | empty |
| 2 | 1025 | 0.79 | 0.80 | 80 | B12, 5AD |
| 3 | 956 | 0.78 | 0.81 | 81 | B12 |
| 4 | 215 | 0.69 | 0.86 | 36 | empty |
| 5 | 254 | 0.65 | 0.82 | 41 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1452 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1413 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 659 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 429 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 405 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5C8A · Crystal structure of a truncated form of thermus thermophilus carh bound to… · 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 Q746J7
- Elsewhere: RCSB PDB 5C8A · PDBe 5C8A · UniProt Q746J7
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