Research workbench
Crystal structure of mtb PKS13 thioesterase domain in complex with compound 6
Analyse Crystal structure of mtb PKS13 thioesterase domain in complex with compound 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M7V
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyketide synthase PKS13
- EC
- 2.3.1.-
- UniProt
- I6X8D2
- Ligands
- Z3J
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyketide synthase PKS13 (EC 2.3.1.-) | protein | 267 | 47% helix, 15% strand | I6X8D2 |
| B | Polyketide synthase PKS13 (EC 2.3.1.-) | protein | 272 | 45% helix, 15% strand | I6X8D2 |
Ligands and binding sites
- Z3J · 5-hydroxy-2-(4-hydroxyphenyl)-N-methyl-4-[(2-oxa-6-azaspiro[3.4]octan-6-yl)methyl]-1-benzofuran-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.71 | 0.79 | 60 | Z3J |
| 2 | 249 | 0.62 | 0.80 | 28 | Z3J |
| 3 | 352 | 0.56 | 0.75 | 36 | empty |
| 4 | 157 | 0.44 | 0.74 | 18 | empty |
| 5 | 97 | 0.39 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 569 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7M7V · Crystal Structure of Mtb Pks13 Thioesterase domain in complex with Compound 6 · the same entry in another collection · chain A against A, TM-score 1.00
- I6X8D2 · AlphaFold monomer V2.0 prediction for polyketide synthase PKS13 (I6X8D2) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 I6X8D2
- Elsewhere: RCSB PDB 7M7V · PDBe 7M7V · UniProt I6X8D2
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