MolNFT v1 · #136789 · protein
Crystal structure of mtb PKS13 thioesterase domain in complex with inhibitor TAM16
5V3Y · Polyketide synthase PKS13 (termination polyketide synthase): “Crystal structure of mtb PKS13 thioesterase domain in complex with inhibitor TAM16”. X-ray diffraction, 2 ligands (5V8, SO4), 8 pockets (best druggability 0.74). MolNFT…
- PDB
- 5V3Y
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyketide synthase PKS13 (termination polyketide synthase)
- EC
- 2.7.7.-
- UniProt
- A0A0T9CRX1
- Ligands
- 5V8, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyketide synthase PKS13 (termination polyketide synthase) (EC 2.7.7.-) | protein | 269 | 47% helix, 15% strand | A0A0T9CRX1 |
| B | Polyketide synthase PKS13 (termination polyketide synthase) (EC 2.7.7.-) | protein | 273 | 46% helix, 15% strand | A0A0T9CRX1 |
Ligands and binding sites
- 5V8 · 2-(4-hydroxyphenyl)-~{N}-methyl-5-oxidanyl-4-(piperidin-1-ylmethyl)-1-benzofuran-3-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.74 | 0.82 | 55 | 5V8 |
| 2 | 537 | 0.66 | 0.77 | 55 | 5V8 |
| 3 | 309 | 0.53 | 0.75 | 28 | empty |
| 4 | 76 | 0.44 | 0.81 | 17 | empty |
| 5 | 133 | 0.44 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 593 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5V3Y · Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM16 · 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 A0A0T9CRX1
- Elsewhere: RCSB PDB 5V3Y · PDBe 5V3Y · UniProt A0A0T9CRX1
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