Research workbench
Crystal structure of the catalytic domain of PBP2 S310A from neisseria gonorrhoeae with the H514A mutation at pH 7.5
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
- 6XQX
- Type
- protein
- Length
- 647 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
- SO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 322 | 36% helix, 19% strand | P08149 |
| B | Probable peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 325 | 37% helix, 22% strand | P08149 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.60 | 0.77 | 26 | EDO |
| 2 | 334 | 0.59 | 0.77 | 40 | SO4 |
| 3 | 175 | 0.45 | 0.75 | 26 | empty |
| 4 | 140 | 0.43 | 0.75 | 24 | empty |
| 5 | 104 | 0.36 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 913 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6XQX · Crystal structure of the catalytic domain of PBP2 S310A from Neisseria gonorrhoeae with… · 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 0.99
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 6XQX · PDBe 6XQX · UniProt P08149
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