Research workbench
Crystal structure of PBP2A clinical mutant N146K from mrsa
Analyse Crystal structure of PBP2A clinical mutant N146K from mrsa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BL3
- Type
- protein
- Length
- 1,279 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
- Q54113
- Ligands
- MUR, CD, CL
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin binding protein 2 prime (EC 3.4.16.4) | protein | 640 | 33% helix, 26% strand | Q54113 |
| B | Penicillin binding protein 2 prime (EC 3.4.16.4) | protein | 639 | 31% helix, 27% strand | Q54113 |
Ligands and binding sites
- MUR · beta-muramic acid · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 7 copies · chains A, B
- CL · Chloride ion · ion · 4 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.77 | 0.79 | 104 | CD, CL, MUR |
| 2 | 369 | 0.65 | 0.80 | 48 | empty |
| 3 | 363 | 0.64 | 0.79 | 36 | empty |
| 4 | 286 | 0.58 | 0.78 | 33 | MUR |
| 5 | 167 | 0.51 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1547 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4BL3 · Crystal structure of PBP2a clinical mutant N146K from MRSA · 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 Q54113
- Elsewhere: RCSB PDB 4BL3 · PDBe 4BL3 · UniProt Q54113
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