MolNFT v1 · #183824 · protein
Crystal structure of penicillin-binding protein 1 (PBP1) from staphylococcus aureus in complex with penicillin G
7O4B: “Crystal structure of penicillin-binding protein 1 (PBP1) from staphylococcus aureus in complex with…”. X-ray diffraction, 2 ligands (PNM, SO4), 7 pockets (best druggability 0.65). MolNFT v1 #183824 on GenesisL1: 3D structure…
- PDB
- 7O4B
- Type
- protein
- Length
- 982 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1
- UniProt
- A0A0H2WVW5
- Ligands
- PNM, SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1 | protein | 503 | 32% helix, 25% strand | A0A0H2WVW5 |
| C | Penicillin-binding protein 1 | protein | 479 | 32% helix, 26% strand | A0A0H2WVW5 |
Ligands and binding sites
- PNM · Open form - penicillin G · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 11 copies · chains A, C
- CIT · Citric acid · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.65 | 0.80 | 37 | PNM |
| 2 | 373 | 0.64 | 0.79 | 58 | SO4 |
| 3 | 248 | 0.57 | 0.78 | 33 | PNM |
| 4 | 106 | 0.42 | 0.77 | 16 | empty |
| 5 | 122 | 0.41 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 759 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7O4B · Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in… · 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 A0A0H2WVW5
- Elsewhere: RCSB PDB 7O4B · PDBe 7O4B · UniProt A0A0H2WVW5
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