Research workbench
Crystal structure of PBP2A from mrsa in the presence of oxacillin ligand
Analyse Crystal structure of PBP2A from mrsa in the presence of oxacillin ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M19
- Type
- protein
- Length
- 1,273 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2
- UniProt
- E2D9B8
- Ligands
- MUR, CD
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2 | protein | 638 | 35% helix, 27% strand | E2D9B8 |
| B | Penicillin-binding protein 2 | protein | 635 | 35% helix, 27% strand | E2D9B8 |
Ligands and binding sites
- MUR · beta-muramic acid · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.75 | 0.80 | 89 | CD |
| 2 | 351 | 0.62 | 0.79 | 46 | empty |
| 3 | 300 | 0.61 | 0.79 | 30 | MUR |
| 4 | 342 | 0.60 | 0.77 | 40 | empty |
| 5 | 120 | 0.58 | 0.85 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1706 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5M19 · Crystal structure of PBP2a from MRSA in the presence of Oxacillin ligand · 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 E2D9B8
- Elsewhere: RCSB PDB 5M19 · PDBe 5M19 · UniProt E2D9B8
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