MolNFT v1 · #53730 · protein
Crystal structure of the methicillin-resistant staphylococcus aureus SAR2676, a pantothenate synthetase.
2X3F · Panthothenate synthetase: “Crystal structure of the methicillin-resistant staphylococcus aureus SAR2676, a pantothenate synthetase.”. X-ray diffraction, 2 ligands (APC, SO4), 4 pockets (best druggability 0.85). MolNFT v1 #53730 on…
- PDB
- 2X3F
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Panthothenate synthetase
- EC
- 6.3.2.1
- UniProt
- Q6GDK5
- Ligands
- APC, SO4
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Panthothenate synthetase (EC 6.3.2.1) | protein | 281 | 44% helix, 22% strand | Q6GDK5 |
| B | Panthothenate synthetase (EC 6.3.2.1) | protein | 281 | 43% helix, 22% strand | Q6GDK5 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
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 | 436 | 0.85 | 0.93 | 65 | APC, SO4 |
| 2 | 552 | 0.82 | 0.88 | 61 | APC |
| 3 | 364 | 0.70 | 0.82 | 43 | empty |
| 4 | 52 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1290 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2X3F · Crystal Structure of the Methicillin-Resistant Staphylococcus aureus Sar2676, a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GDK5 · AlphaFold monomer V2.0 prediction for pantothenate synthetase (Q6GDK5) · 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 Q6GDK5
- Elsewhere: RCSB PDB 2X3F · PDBe 2X3F · UniProt Q6GDK5
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