MolNFT v1 · #145699 · protein
Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine
6CVU · ATP-dependent dethiobiotin synthetase biod: “Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine”. X-ray diffraction, 2 ligands (CTN, SO4), 7 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 6CVU
- Type
- protein
- Length
- 908 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent dethiobiotin synthetase biod
- UniProt
- A5U2S7
- Ligands
- CTN, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent dethiobiotin synthetase biod | protein | 227 | 42% helix, 26% strand | A5U2S7 |
| B | ATP-dependent dethiobiotin synthetase biod | protein | 226 | 42% helix, 25% strand | A5U2S7 |
| C | ATP-dependent dethiobiotin synthetase biod | protein | 228 | 41% helix, 24% strand | A5U2S7 |
| D | ATP-dependent dethiobiotin synthetase biod | protein | 227 | 42% helix, 26% strand | A5U2S7 |
Ligands and binding sites
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.72 | 0.77 | 73 | empty |
| 2 | 308 | 0.64 | 0.81 | 53 | SO4, CTN |
| 3 | 265 | 0.61 | 0.80 | 52 | SO4, CTN |
| 4 | 250 | 0.61 | 0.80 | 44 | SO4 |
| 5 | 203 | 0.60 | 0.82 | 33 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 1180 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1170 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 99 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 81 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CVU · Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- A5U2S7 · AlphaFold monomer V2.0 prediction for ATP-dependent dethiobiotin synthetase biod (A5U2S7) · a predicted model of the same protein · chain B 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 A5U2S7
- Elsewhere: RCSB PDB 6CVU · PDBe 6CVU · UniProt A5U2S7
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