MolNFT v1 · #15361 · protein
Crystal structure of a pantothenate synthetase from M. tuberculosis in complex with ampcpp and pantoate
1N2E: “Crystal structure of a pantothenate synthetase from M. tuberculosis in complex with ampcpp and pantoate”. X-ray diffraction, 4 ligands (APC, PAF, MG), 4 pockets (best druggability 0.81). MolNFT v1 #15361 on GenesisL1: 3D structure…
- PDB
- 1N2E
- Type
- protein
- Length
- 569 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, PAF, MG, SO4
- Pockets
- 4 · best druggability 0.81
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 | 288 | 43% helix, 22% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 281 | 43% helix, 23% strand | P0A5R0 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- PAF · Pantoate · ligand · chains A
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EOH · Ethanol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.81 | 0.87 | 57 | MG, APC, GOL |
| 2 | 595 | 0.81 | 0.86 | 57 | APC, PAF |
| 3 | 271 | 0.60 | 0.79 | 28 | EOH |
| 4 | 60 | 0.32 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1219 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1N2E · Crystal Structure of a Pantothenate Synthetase from M. tuberculosis in complex with… · 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 1N2E · PDBe 1N2E · UniProt P0A5R0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.