MolNFT v1 · #158204 · protein
Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine and fragment degradation product B9D
6NN0 · ATP-dependent dethiobiotin synthetase biod: “Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine and…”. X-ray diffraction, 4 ligands (KSJ, KSP, CTN), 6 pockets (best druggability…
- PDB
- 6NN0
- Type
- protein
- Length
- 907 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
- P9WPQ5
- Ligands
- KSJ, KSP, CTN, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 41% helix, 22% strand | P9WPQ5 |
| B | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 226 | 42% helix, 24% strand | P9WPQ5 |
| D | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 43% helix, 22% strand | P9WPQ5 |
Ligands and binding sites
- KSJ · [(1S,2R)-2-(2-hydroxybenzene-1-carbonyl) cyclopentyl]acetic acid · ligand · 4 copies · chains A, B, C, D
- KSP · [(1R,2S)-2-(2-hydroxybenzene-1-carbonyl) cyclopentyl]acetic acid · ligand · 4 copies · chains A, B, C, D
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.78 | 0.80 | 93 | SO4, KSJ, KSP |
| 2 | 316 | 0.66 | 0.81 | 44 | SO4, KSJ, KSP |
| 3 | 344 | 0.65 | 0.80 | 46 | SO4, KSJ, KSP |
| 4 | 304 | 0.65 | 0.81 | 45 | SO4, KSJ, KSP |
| 5 | 137 | 0.40 | 0.74 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1111 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1062 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 127 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 114 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NN0 · Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WPQ5 · AlphaFold monomer V2.0 prediction for dethiobiotin synthetase biod (P9WPQ5) · 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 P9WPQ5
- Elsewhere: RCSB PDB 6NN0 · PDBe 6NN0 · UniProt P9WPQ5
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