Research workbench
Crystal structure of pantothenate synthetase from staphylococcus aureus in complex with pantoyl adenylate
Analyse Crystal structure of pantothenate synthetase from staphylococcus aureus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AG6
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate synthetase
- EC
- 6.3.2.1
- UniProt
- Q2FV22
- Ligands
- PAJ
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pantothenate synthetase (EC 6.3.2.1) | protein | 283 | 43% helix, 22% strand | Q2FV22 |
Ligands and binding sites
- PAJ · Pantoyl adenylate · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 8 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
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 | 442 | 0.85 | 0.92 | 67 | PAJ, ACY |
| 2 | 404 | 0.85 | 0.93 | 67 | PAJ, ACY |
| 3 | 175 | 0.73 | 0.90 | 31 | empty |
| 4 | 67 | 0.28 | 0.73 | 20 | PG4 |
| 5 | 59 | 0.28 | 0.74 | 12 | PG4 |
Interfaces
1 interface between chains.
- A–B · 1423 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3AG6 · Crystal Structure of Pantothenate Synthetase from Staphylococcus aureus in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2FV22 · AlphaFold monomer V2.0 prediction for pantothenate synthetase (Q2FV22) · a predicted model of the same protein · chain A 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 Q2FV22
- Elsewhere: RCSB PDB 3AG6 · PDBe 3AG6 · UniProt Q2FV22
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