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Crystal structure of the catalytic domain of PBP2 S310A from neisseria gonorrhoeae 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
- 6XQZ
- Type
- protein
- Length
- 635 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
- CL, SO4
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 322 | 37% helix, 20% strand | P08149 |
| B | Peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 313 | 38% helix, 19% strand | P08149 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.59 | 0.76 | 30 | empty |
| 2 | 271 | 0.58 | 0.78 | 35 | SO4 |
| 3 | 93 | 0.52 | 0.83 | 21 | empty |
| 4 | 123 | 0.51 | 0.81 | 21 | empty |
| 5 | 172 | 0.47 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 956 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6XQZ · Crystal structure of the catalytic domain of PBP2 S310A from Neisseria gonorrhoeae at pH… · 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 6XQZ · PDBe 6XQZ · UniProt P08149
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