MolNFT v1 · #126377 · protein
Crystal structure of PBP2A from mrsa in the presence of cefepime ligand
5M18 · Penicillin-binding protein 2: “Crystal structure of PBP2A from mrsa in the presence of cefepime ligand”. X-ray diffraction, 2 ligands (MUR, CD), 16 pockets (best druggability 0.77). MolNFT v1 #126377 on GenesisL1: 3D structure…
- PDB
- 5M18
- Type
- protein
- Length
- 1,275 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 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2 | protein | 640 | 34% helix, 27% strand | E2D9B8 |
| B | Penicillin-binding protein 2 | protein | 635 | 34% helix, 26% strand | E2D9B8 |
Ligands and binding sites
- MUR · beta-muramic acid · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 5 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.77 | 0.82 | 83 | MUR |
| 2 | 439 | 0.62 | 0.77 | 58 | empty |
| 3 | 210 | 0.60 | 0.81 | 23 | MUR |
| 4 | 319 | 0.60 | 0.78 | 39 | empty |
| 5 | 161 | 0.52 | 0.79 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1648 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5M18 · Crystal structure of PBP2a from MRSA in the presence of Cefepime 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 5M18 · PDBe 5M18 · UniProt E2D9B8
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