Research workbench
Crystal structure of thermus thermophilus carh bound to adenosylcobalamin and a 26-bp DNA segment
Analyse Crystal structure of thermus thermophilus carh bound to adenosylcobalamin and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C8E
- Type
- protein + DNA
- Length
- 2,161 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light-dependent transcriptional regulator carh; 26-mer DNA segment containing the carh…
- UniProt
- Q746J7
- Ligands
- B12, 5AD
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 10 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light-dependent transcriptional regulator carh | protein | 273 | 55% helix, 9% strand | Q746J7 |
| B | Light-dependent transcriptional regulator carh | protein | 276 | 56% helix, 10% strand | Q746J7 |
| C | Light-dependent transcriptional regulator carh | protein | 279 | 55% helix, 9% strand | Q746J7 |
| D | Light-dependent transcriptional regulator carh | protein | 205 | 53% helix, 10% strand | Q746J7 |
| E | Light-dependent transcriptional regulator carh | protein | 273 | 55% helix, 9% strand | Q746J7 |
| F | Light-dependent transcriptional regulator carh | protein | 270 | 55% helix, 9% strand | Q746J7 |
| G | Light-dependent transcriptional regulator carh | protein | 280 | 54% helix, 9% strand | Q746J7 |
| H | Light-dependent transcriptional regulator carh | protein | 201 | 56% helix, 10% strand | Q746J7 |
| I, K | 26-mer DNA segment containing the carh operator sequence (antisense strand) | dna | 26 | — | — |
| J, L | 26-mer DNA segment containing the carh operator sequence (sense strand) | dna | 26 | — | — |
Ligands and binding sites
- B12 · Cobalamin · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 5AD · 5'-deoxyadenosine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 1042 | 0.79 | 0.80 | 91 | B12 |
| 2 | 702 | 0.78 | 0.83 | 80 | empty |
| 3 | 640 | 0.78 | 0.83 | 81 | empty |
| 4 | 749 | 0.78 | 0.82 | 82 | B12 |
| 5 | 1116 | 0.77 | 0.79 | 83 | B12, 5AD |
Interfaces
30 interfaces between chains.
- E–F · 1553 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1526 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1414 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1400 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1152 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5C8E · Crystal structure of Thermus thermophilus CarH bound to adenosylcobalamin and a 26-bp DNA… · 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 5C8E · PDBe 5C8E · UniProt Q746J7
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