Research workbench
Crystal structure of a pantothenate synthetase from M. tuberculosis in complex with ampcpp
Analyse Crystal structure of a pantothenate synthetase from M. tuberculosis in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N2G
- Type
- protein
- Length
- 573 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate synthetase
- EC
- 6.3.2.1
- UniProt
- P0A5R0
- Ligands
- APC, MG, SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate synthetase (EC 6.3.2.1) | protein | 289 | 43% helix, 22% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 284 | 43% helix, 23% strand | P0A5R0 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- EOH · Ethanol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.82 | 0.87 | 56 | MG, APC, GOL |
| 2 | 539 | 0.81 | 0.87 | 55 | MG, APC, GOL |
| 3 | 168 | 0.52 | 0.79 | 23 | GOL |
| 4 | 74 | 0.38 | 0.78 | 16 | empty |
| 5 | 76 | 0.36 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1239 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1N2G · Crystal Structure of a Pantothenate Synthetase from M. tuberculosis in complex with AMPCPP · the same entry in another collection · 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 P0A5R0
- Elsewhere: RCSB PDB 1N2G · PDBe 1N2G · UniProt P0A5R0
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