MolNFT v1 · #169920 · protein
Crystal structure of the catalytic domain of PBP2 S310A from neisseria gonorrhoeae at pH 7.5
6XQZ · Peptidoglycan D,D-transpeptidase pena: “Crystal structure of the catalytic domain of PBP2 S310A from neisseria gonorrhoeae at pH 7.5”. X-ray diffraction, 2 ligands (CL, SO4), 8 pockets (best druggability 0.59). MolNFT v1 #169920 on…
- 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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