Research workbench
Structure of pbp-a, L158E mutant. acyl-enzyme complex with penicillin- G.
Analyse Structure of pbp-a, L158E mutant. acyl-enzyme complex with penicillin- G. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JBF
- Type
- protein
- Length
- 1,067 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TLL2115 protein
- EC
- 3.4.16.4
- UniProt
- Q8DH45
- Ligands
- PNM
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | TLL2115 protein (EC 3.4.16.4) | protein | 264 | 42% helix, 20% strand | Q8DH45 |
| B | TLL2115 protein (EC 3.4.16.4) | protein | 265 | 42% helix, 20% strand | Q8DH45 |
| D | TLL2115 protein (EC 3.4.16.4) | protein | 274 | 41% helix, 19% strand | Q8DH45 |
Ligands and binding sites
- PNM · Open form - penicillin G · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.71 | 0.78 | 52 | PNM |
| 2 | 694 | 0.70 | 0.78 | 68 | PNM |
| 3 | 160 | 0.52 | 0.79 | 31 | PNM |
| 4 | 190 | 0.50 | 0.77 | 21 | empty |
| 5 | 107 | 0.35 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 365 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 289 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 173 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2JBF · Structure of PBP-A, L158E mutant. Acyl-enzyme complex with penicillin- G. · 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 Q8DH45
- Elsewhere: RCSB PDB 2JBF · PDBe 2JBF · UniProt Q8DH45
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