MolNFT v1 · #72435 · protein
Crystal structure of pantoate-beta-alanine ligase from francisella tularensis
3N8H · Pantothenate synthetase: “Crystal structure of pantoate-beta-alanine ligase from francisella tularensis”. X-ray diffraction, 2 ligands (PRO, AMP), 5 pockets (best druggability 0.86). MolNFT v1 #72435 on GenesisL1: 3D structure…
- PDB
- 3N8H
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate synthetase
- EC
- 6.3.2.1
- UniProt
- Q5NF57
- Ligands
- PRO, AMP
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pantothenate synthetase (EC 6.3.2.1) | protein | 262 | 42% helix, 23% strand | Q5NF57 |
Ligands and binding sites
- PRO · Proline · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.86 | 0.94 | 64 | PRO, AMP, GOL |
| 2 | 406 | 0.84 | 0.93 | 58 | PRO, AMP, GOL |
| 3 | 429 | 0.60 | 0.76 | 36 | empty |
| 4 | 78 | 0.36 | 0.76 | 18 | empty |
| 5 | 58 | 0.31 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1326 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3N8H · Crystal Structure of Pantoate-beta-alanine Ligase from Francisella tularensis · the same entry in another collection · chain B against B, TM-score 1.00
- Q5NF57 · AlphaFold monomer V2.0 prediction for pantothenate synthetase (Q5NF57) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5NF57
- Elsewhere: RCSB PDB 3N8H · PDBe 3N8H · UniProt Q5NF57
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