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Crystal structure of pantoate-beta-alanine ligase from francisella tularensis complexed with beta-gamma ATP and beta-alanine
Analyse Crystal structure of pantoate-beta-alanine ligase from francisella tularensis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QTT
- Type
- protein
- Length
- 520 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
- ANP, PRO, BAL, MG
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate synthetase (EC 6.3.2.1) | protein | 261 | 43% helix, 21% strand | Q5NF57 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 259 | 42% helix, 21% strand | Q5NF57 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- PRO · Proline · ligand · 2 copies · chains A, B
- BAL · Beta-alanine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
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 | 368 | 0.85 | 0.94 | 49 | PRO, ANP, BAL |
| 2 | 445 | 0.85 | 0.92 | 60 | ANP, PRO, MG, BAL |
| 3 | 1078 | 0.75 | 0.78 | 84 | empty |
| 4 | 61 | 0.35 | 0.78 | 17 | empty |
| 5 | 61 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3QTT · Crystal Structure of Pantoate-beta-alanine Ligase from Francisella tularensis Complexed… · the same entry in another collection · chain A against A, 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 3QTT · PDBe 3QTT · UniProt Q5NF57
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