Research workbench
Penicillin-binding protein 1A (pbp 1A) acyl-enzyme complex (biapenem) from streptococcus pneumoniae
Analyse Penicillin-binding protein 1A (pbp 1A) acyl-enzyme complex (biapenem) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZC5
- Type
- protein
- Length
- 800 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1A
- UniProt
- Q8DR59, Q549Y6
- Ligands
- BMG, ZN
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Penicillin-binding protein 1A | protein | 16 | 0% helix, 44% strand | Q8DR59 |
| B, D | Penicillin-binding protein 1A | protein | 384 | 33% helix, 21% strand | Q549Y6 |
Ligands and binding sites
- BMG · (4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-meth yl-4,5-dihydro-1H-pyrrole-2-carboxylate · ligand · 2 copies · chains B, D
- ZN · Zinc ion · metal · 8 copies · chains B, D
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 | 500 | 0.65 | 0.77 | 58 | BMG |
| 2 | 509 | 0.65 | 0.77 | 56 | BMG |
| 3 | 151 | 0.51 | 0.79 | 28 | empty |
| 4 | 154 | 0.49 | 0.78 | 21 | empty |
| 5 | 157 | 0.45 | 0.76 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 769 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 730 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2ZC5 · Penicillin-binding protein 1A (PBP 1A) acyl-enzyme complex (biapenem) from Streptococcus… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8DR59 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 1A (Q8DR59) · a predicted model of the same protein · chain A against A, TM-score 0.63
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
- Every structure of UniProt Q549Y6
- Elsewhere: RCSB PDB 2ZC5 · PDBe 2ZC5 · UniProt Q8DR59 · UniProt Q549Y6
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