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Crystal structure of transpeptidase domain of PBP2 from neisseria gonorrhoeae acylated by cefixime
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
- 6P55
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan D,D-transpeptidase pena
- EC
- 3.4.16.4
- UniProt
- P08149
- Ligands
- NZM, PO4
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 326 | 37% helix, 22% strand | P08149 |
| B | Peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 327 | 36% helix, 21% strand | P08149 |
Ligands and binding sites
- NZM · cefixime, bound form · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.61 | 0.78 | 30 | empty |
| 2 | 354 | 0.60 | 0.77 | 41 | NZM, PEG |
| 3 | 318 | 0.59 | 0.77 | 45 | NZM, PEG |
| 4 | 141 | 0.54 | 0.81 | 24 | empty |
| 5 | 146 | 0.51 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1017 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6P55 · 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 6P55 · PDBe 6P55 · UniProt P08149
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