MolNFT v1 · #108998 · protein
Nucleotide triphosphate promiscuity in mycobacterium tuberculosis dethiobiotin synthetase
4WOP · ATP-dependent dethiobiotin synthetase biod: “Nucleotide triphosphate promiscuity in mycobacterium tuberculosis dethiobiotin synthetase”. X-ray diffraction, 2 ligands (CTP, SO4), 7 pockets (best druggability 0.80). MolNFT v1 #108998…
- PDB
- 4WOP
- Type
- protein
- Length
- 900 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent dethiobiotin synthetase biod
- EC
- 6.3.3.3
- UniProt
- A5U2S7
- Ligands
- CTP, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 225 | 43% helix, 23% strand | A5U2S7 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 3 copies · chains A, C, D
- SO4 · Sulfate ion · ion · 5 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.80 | 0.84 | 96 | SO4 |
| 2 | 197 | 0.66 | 0.85 | 44 | SO4 |
| 3 | 314 | 0.63 | 0.80 | 50 | SO4, CTP |
| 4 | 171 | 0.55 | 0.80 | 33 | CTP, SO4 |
| 5 | 109 | 0.44 | 0.78 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1238 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1160 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 359 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 125 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4WOP · Nucleotide Triphosphate Promiscuity in Mycobacterium tuberculosis Dethiobiotin Synthetase · 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 D 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 A5U2S7
- Elsewhere: RCSB PDB 4WOP · PDBe 4WOP · UniProt A5U2S7
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