Research workbench
Penicillin binding protein 2X (PBP2X) from S.PNEUMONIAE in complex with oxacillin and a tetrasaccharide
Analyse Penicillin binding protein 2X (PBP2X) from S.PNEUMONIAE in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OJ1
- Type
- protein
- Length
- 675 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2X
- UniProt
- P59676
- Ligands
- 1S6, NA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2X | protein | 675 | 29% helix, 22% strand | P59676 |
Ligands and binding sites
- 1S6 · (2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.74 | 0.86 | 51 | empty |
| 2 | 482 | 0.67 | 0.78 | 58 | 1S6, NA |
| 3 | 146 | 0.52 | 0.79 | 28 | empty |
| 4 | 189 | 0.47 | 0.75 | 30 | empty |
| 5 | 75 | 0.34 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5OJ1 · Penicillin Binding Protein 2x (PBP2x) from S.pneumoniae in complex with Oxacillin and a… · the same entry in another collection · chain A against A, TM-score 1.00
- P59676 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 2X (P59676) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P59676
- Elsewhere: RCSB PDB 5OJ1 · PDBe 5OJ1 · UniProt P59676
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