MolNFT v1 · #82618 · protein
Crystal structure of penicillin-binding protein 3 (PBP3) from methicilin-resistant staphylococcus aureus in the cefotaxime bound form.
3VSL: “Crystal structure of penicillin-binding protein 3 (PBP3) from methicilin-resistant staphylococcus aureus in…”. X-ray diffraction, 1 ligand (CEF), 12 pockets (best druggability 0.78). MolNFT v1 #82618 on GenesisL1: 3D structure…
- PDB
- 3VSL
- Type
- protein
- Length
- 1,262 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 3
- UniProt
- Q8NWC2
- Ligands
- CEF
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 3 | protein | 631 | 33% helix, 23% strand | Q8NWC2 |
| B | Penicillin-binding protein 3 | protein | 631 | 31% helix, 20% strand | Q8NWC2 |
Ligands and binding sites
- CEF · CEFOTAXIME, C3' cleaved, open, bound form · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.78 | 0.81 | 67 | empty |
| 2 | 707 | 0.78 | 0.82 | 52 | empty |
| 3 | 706 | 0.77 | 0.82 | 52 | empty |
| 4 | 714 | 0.70 | 0.77 | 78 | empty |
| 5 | 101 | 0.64 | 0.89 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2346 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3VSL · Crystal structure of penicillin-binding protein 3 (PBP3) from methicilin-resistant… · the same entry in another collection · chain B against B, 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 Q8NWC2
- Elsewhere: RCSB PDB 3VSL · PDBe 3VSL · UniProt Q8NWC2
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