Research workbench
Crystal structure of transpeptidase domain of PBP2 from neisseria gonorrhoeae acylated by ceftriaxone
Analyse Crystal structure of transpeptidase domain of PBP2 from neisseria gonorrhoeae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P54
- Type
- protein
- Length
- 651 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable peptidoglycan D,D-transpeptidase pena
- EC
- 3.4.16.4
- UniProt
- P08149
- Ligands
- NZV, CEF, 9F2
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 325 | 36% helix, 22% strand | P08149 |
| B | Probable peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 326 | 37% helix, 22% strand | P08149 |
Ligands and binding sites
- NZV · ceftriaxone, bound form · ligand · chains A
- CEF · CEFOTAXIME, C3' cleaved, open, bound form · ligand · chains B
- 9F2 · Ceftriaxone · ligand · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.63 | 0.79 | 44 | CEF, PEG |
| 2 | 399 | 0.63 | 0.78 | 43 | NZV |
| 3 | 374 | 0.62 | 0.77 | 26 | empty |
| 4 | 116 | 0.53 | 0.82 | 23 | empty |
| 5 | 144 | 0.52 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1003 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6P54 · Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae acylated by… · the same entry in another collection · chain A against A, TM-score 1.00
- P08149 · AlphaFold monomer V2.0 prediction for probable peptidoglycan D,D-transpeptidase pena… · 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 P08149
- Elsewhere: RCSB PDB 6P54 · PDBe 6P54 · UniProt P08149
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.