Research workbench
Crystal structure of the methicillin-resistant staphylococcus aureus SAR2028, an ASPARTATE_TYROSINE_PHENYLALANINE pyridoxal-5'-phosphate dependent aminotransferase
Analyse Crystal structure of the methicillin-resistant staphylococcus aureus SAR2028… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X5F
- Type
- protein
- Length
- 856 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASPARTATE_TYROSINE_PHENYLALANINE pyridoxal-5' phosphate-dependent aminotransferase
- UniProt
- Q6GFC0
- Ligands
- PLP, MG, PO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASPARTATE_TYROSINE_PHENYLALANINE pyridoxal-5' phosphate-dependent aminotransferase | protein | 428 | 48% helix, 16% strand | Q6GFC0 |
| B | ASPARTATE_TYROSINE_PHENYLALANINE pyridoxal-5' phosphate-dependent aminotransferase | protein | 428 | 47% helix, 16% strand | Q6GFC0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.75 | 0.81 | 61 | PLP |
| 2 | 647 | 0.75 | 0.81 | 57 | PLP |
| 3 | 367 | 0.63 | 0.79 | 28 | MG |
| 4 | 150 | 0.51 | 0.79 | 22 | empty |
| 5 | 183 | 0.50 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 4511 Ų buried · 97 hydrogen bonds · protein-protein
Compared structures
- 2X5F · Crystal structure of the methicillin-resistant Staphylococcus aureus Sar2028, an… · 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 Q6GFC0
- Elsewhere: RCSB PDB 2X5F · PDBe 2X5F · UniProt Q6GFC0
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