Research workbench
GSK3011724A cocrystallised with mycobacterium tuberculosis H37RV kasa
Analyse GSK3011724A cocrystallised with mycobacterium tuberculosis H37RV kasa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LD8
- Type
- protein
- Length
- 826 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 1
- EC
- 2.3.1.41
- UniProt
- P9WQD9
- Ligands
- 6U5, NA
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-[acyl-carrier-protein] synthase 1 (EC 2.3.1.41) | protein | 413 | 39% helix, 20% strand | P9WQD9 |
Ligands and binding sites
- 6U5 · ~{N}-(1-methylindazol-6-yl)butane-1-sulfonamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.79 | 0.87 | 44 | PG4, 6U5 |
| 2 | 418 | 0.77 | 0.86 | 45 | 6U5, PG4 |
| 3 | 132 | 0.65 | 0.87 | 36 | empty |
| 4 | 127 | 0.63 | 0.87 | 37 | empty |
| 5 | 52 | 0.33 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 3344 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 5LD8 · GSK3011724A cocrystallised with Mycobacterium tuberculosis H37Rv KasA · the same entry in another collection · chain A against A, TM-score 1.00
- P9WQD9 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 1… · a predicted model of the same protein · 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 P9WQD9
- Elsewhere: RCSB PDB 5LD8 · PDBe 5LD8 · UniProt P9WQD9
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