Research workbench
Penicillin-binding protein 1A (pbp-1A) acyl-enzyme complex (cefotaxime) from streptococcus pneumoniae
Analyse Penicillin-binding protein 1A (pbp-1A) acyl-enzyme complex (cefotaxime) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C5W
- Type
- protein
- Length
- 401 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1A
- UniProt
- Q8DR59
- Ligands
- CEF, ZN, CL
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1A | protein | 16 | 0% helix, 44% strand | Q8DR59 |
| B | Penicillin-binding protein 1A | protein | 385 | 34% helix, 21% strand | Q8DR59 |
Ligands and binding sites
- CEF · CEFOTAXIME, C3' cleaved, open, bound form · ligand · chains B
- ZN · Zinc ion · metal · 5 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.62 | 0.77 | 45 | EDO, CEF |
| 2 | 127 | 0.51 | 0.81 | 23 | empty |
| 3 | 86 | 0.41 | 0.78 | 15 | empty |
| 4 | 59 | 0.28 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 750 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2C5W · Penicillin-binding protein 1A (pbp-1A) acyl-enzyme complex (cefotaxime) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8DR59 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 1A (Q8DR59) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8DR59
- Elsewhere: RCSB PDB 2C5W · PDBe 2C5W · UniProt Q8DR59
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