MolNFT v1 · #96125 · protein
Crystal structure of mycobacterium tuberculosis PKS11 reveals intermediates in the synthesis of methyl-branched alkylpyrones
4JAP · Alpha-pyrone synthesis polyketide synthase-like PKS11: “Crystal structure of mycobacterium tuberculosis PKS11 reveals intermediates in the synthesis of…”. X-ray diffraction, 3 ligands (PLM, COA, 14U), 11 pockets (best druggability…
- PDB
- 4JAP
- Type
- protein
- Length
- 1,410 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-pyrone synthesis polyketide synthase-like PKS11
- EC
- 2.3.1.-
- UniProt
- O06587
- Ligands
- PLM, COA, 14U
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | Alpha-pyrone synthesis polyketide synthase-like PKS11 (EC 2.3.1.-) | protein | 352 | 44% helix, 25% strand | O06587 |
| C, A | Alpha-pyrone synthesis polyketide synthase-like PKS11 (EC 2.3.1.-) | protein | 353 | 46% helix, 26% strand | O06587 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains D, C
- COA · Coenzyme A · ligand · 2 copies · chains C, B
- 14U · (2S)-2-methyl-3-oxooctadecanoic acid · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.82 | 0.90 | 54 | PLM |
| 2 | 411 | 0.81 | 0.89 | 55 | PLM, COA |
| 3 | 420 | 0.81 | 0.89 | 56 | 14U, COA |
| 4 | 426 | 0.81 | 0.88 | 55 | 14U |
| 5 | 752 | 0.77 | 0.81 | 60 | empty |
Interfaces
5 interfaces between chains.
- B–A · 2174 Ų buried · 17 hydrogen bonds · protein-protein
- D–C · 2171 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 503 Ų buried · 11 hydrogen bonds · protein-protein
- D–B · 327 Ų buried · 3 hydrogen bonds · protein-protein
- C–A · 273 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4JAP · Crystal Structure of Mycobacterium tuberculosis PKS11 Reveals Intermediates in the… · the same entry in another collection · chain D against D, 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 O06587
- Elsewhere: RCSB PDB 4JAP · PDBe 4JAP · UniProt O06587
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