Research workbench
Complex between penicillin-binding protein (PBP2) and mrec from helicobacter pylori
Analyse Complex between penicillin-binding protein (PBP2) and mrec from helicobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LP5
- Type
- protein
- Length
- 1,690 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2 (PBP2); Rod shape-determining protein (mrec)
- UniProt
- O26085, O25924
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2 (PBP2) | protein | 535 | 34% helix, 22% strand | O26085 |
| B | Penicillin-binding protein 2 (PBP2) | protein | 530 | 35% helix, 22% strand | O26085 |
| C | Rod shape-determining protein (mrec) | protein | 157 | 3% helix, 50% strand | O25924 |
| D, E, F | Rod shape-determining protein (mrec) | protein | 156 | 3% helix, 50% strand | O25924 |
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.77 | 0.79 | 91 | empty |
| 2 | 1185 | 0.75 | 0.77 | 98 | empty |
| 3 | 551 | 0.68 | 0.78 | 51 | empty |
| 4 | 264 | 0.54 | 0.76 | 29 | empty |
| 5 | 182 | 0.48 | 0.76 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1055 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 961 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 925 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 857 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 725 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5LP5 · Complex between Penicillin-Binding Protein (PBP2) and MreC 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
- Every structure of UniProt O25924
- Elsewhere: RCSB PDB 5LP5 · PDBe 5LP5 · UniProt O26085 · UniProt O25924
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