Research workbench
Crystal structure of the catalytic domain of PBP2 S310A from neisseria gonorrhoeae in a pre-acylation complex with ceftriaxone
Analyse Crystal structure of the catalytic domain of PBP2 S310A from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XQV
- Type
- protein
- Length
- 654 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
- 9F2, SO4, CL
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 327 | 35% helix, 22% strand | P08149 |
Ligands and binding sites
- 9F2 · Ceftriaxone · ligand · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A
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 | 427 | 0.64 | 0.78 | 42 | 9F2 |
| 2 | 370 | 0.64 | 0.79 | 48 | 9F2 |
| 3 | 371 | 0.60 | 0.77 | 30 | empty |
| 4 | 128 | 0.54 | 0.82 | 23 | empty |
| 5 | 124 | 0.50 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 910 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6XQV · Crystal structure of the catalytic domain of PBP2 S310A from Neisseria gonorrhoeae in a… · 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 A against A, TM-score 0.98
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 6XQV · PDBe 6XQV · UniProt P08149
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.