Research workbench
Crystal structure of mycobacterium tuberculosis PKS11 reveals intermediates in the synthesis of methyl-branched alkylpyrones
Analyse Crystal structure of mycobacterium tuberculosis PKS11 reveals intermediates in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JAQ
- Type
- protein
- Length
- 1,408 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
- 14V, COA, PLM
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, C, B | Alpha-pyrone synthesis polyketide synthase-like PKS11 (EC 2.3.1.-) | protein | 352 | 45% helix, 25% strand | O06587 |
Ligands and binding sites
- 14V · 3,5-dioxoicosanoic acid · ligand · 2 copies · chains A, D
- COA · Coenzyme A · ligand · 2 copies · chains C, B
- PLM · Palmitic acid · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.82 | 0.89 | 54 | COA, PLM |
| 2 | 429 | 0.82 | 0.89 | 57 | COA, PLM |
| 3 | 441 | 0.81 | 0.89 | 54 | 14V |
| 4 | 421 | 0.81 | 0.88 | 56 | 14V |
| 5 | 1141 | 0.79 | 0.81 | 111 | empty |
Interfaces
5 interfaces between chains.
- D–C · 2168 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2135 Ų buried · 20 hydrogen bonds · protein-protein
- D–A · 408 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 5 hydrogen bonds · protein-protein
- D–B · 210 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 lipid (covalent ligand, palmitoylation).
Compared structures
- 4JAQ · 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 4JAQ · PDBe 4JAQ · UniProt O06587
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.