Research workbench
Penicillin-binding protein (PBP2) from helicobacter pylori
Analyse Penicillin-binding protein (PBP2) from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LP4
- Type
- protein
- Length
- 1,047 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2 (PBP2)
- UniProt
- O26085
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2 (PBP2) | protein | 525 | 34% helix, 23% strand | O26085 |
| B | Penicillin-binding protein 2 (PBP2) | protein | 522 | 33% helix, 23% strand | O26085 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.86 | 0.93 | 59 | SO4 |
| 2 | 299 | 0.55 | 0.76 | 37 | empty |
| 3 | 298 | 0.53 | 0.74 | 43 | empty |
| 4 | 165 | 0.47 | 0.76 | 17 | empty |
| 5 | 169 | 0.43 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1974 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5LP4 · Penicillin-Binding Protein (PBP2) from Helicobacter pylori · 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 O26085
- Elsewhere: RCSB PDB 5LP4 · PDBe 5LP4 · UniProt O26085
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