Research workbench
Crystal structure of mycobacterium tuberculosis C171Q kasa variant
Analyse Crystal structure of mycobacterium tuberculosis C171Q kasa variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WGF
- Type
- protein
- Length
- 3,320 residues
- Chains
- 8
- 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
- P63454
- Ligands
- NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | 3-oxoacyl-[acyl-carrier-protein] synthase 1 (EC 2.3.1.41) | protein | 415 | 38% helix, 20% strand | P63454 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- PG4 · Tetraethylene glycol · additive · 7 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.81 | 0.83 | 114 | empty |
| 2 | 1092 | 0.80 | 0.82 | 98 | empty |
| 3 | 427 | 0.80 | 0.87 | 44 | PG4 |
| 4 | 437 | 0.79 | 0.87 | 43 | empty |
| 5 | 499 | 0.79 | 0.86 | 55 | PG4 |
Interfaces
9 interfaces between chains.
- G–H · 3331 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 3313 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 3307 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 3280 Ų buried · 38 hydrogen bonds · protein-protein
- B–F · 330 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2WGF · Crystal structure of Mycobacterium tuberculosis C171Q KasA variant · 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 P63454
- Elsewhere: RCSB PDB 2WGF · PDBe 2WGF · UniProt P63454
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