Research workbench
Crystal structure of PBP2A from mrsa in complex with piperacillin at active site.
Analyse Crystal structure of PBP2A from mrsa in complex with piperacillin at active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H5O
- Type
- protein
- Length
- 1,234 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin binding protein 2 prime
- EC
- 3.4.16.4
- UniProt
- A0A0J9X1X5
- Ligands
- JPP, CD
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin binding protein 2 prime (EC 3.4.16.4) | protein | 598 | 35% helix, 27% strand | A0A0J9X1X5 |
| B | Penicillin binding protein 2 prime (EC 3.4.16.4) | protein | 636 | 34% helix, 26% strand | A0A0J9X1X5 |
Ligands and binding sites
- JPP · Piperacillin (Open Form) · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.81 | 0.83 | 98 | CD |
| 2 | 544 | 0.66 | 0.77 | 70 | CD |
| 3 | 57 | 0.65 | 0.94 | 24 | empty |
| 4 | 512 | 0.63 | 0.76 | 47 | empty |
| 5 | 232 | 0.58 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1668 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6H5O · Crystal structure of PBP2a from MRSA in complex with piperacillin at active site. · 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 A0A0J9X1X5
- Elsewhere: RCSB PDB 6H5O · PDBe 6H5O · UniProt A0A0J9X1X5
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