Research workbench
Crystal structure of mtb PKS13 thioesterase domain in complex with inhibitor TAM16
Analyse Crystal structure of mtb PKS13 thioesterase domain in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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