MolNFT v1 · #169918 · protein
Crystal structure of the catalytic domain of PBP2 S310A from neisseria gonorrhoeae with the H514A mutation at pH 7.5
6XQX · Probable peptidoglycan D,D-transpeptidase pena: “Crystal structure of the catalytic domain of PBP2 S310A from neisseria gonorrhoeae with the H514A mutation at…”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.60).…
- 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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