MolNFT v1 · #150837 · protein
Crystal structure of PBP2A from mrsa in complex with piperacillin at active site.
6H5O · Penicillin binding protein 2 prime: “Crystal structure of PBP2A from mrsa in complex with piperacillin at active site.”. X-ray diffraction, 2 ligands (JPP, CD), 15 pockets (best druggability 0.81). MolNFT v1 #150837 on GenesisL1: 3D…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.