MolNFT v1 · #159913 · protein
Crystal structure of transpeptidase domain of PBP2 from neisseria gonorrhoeae with a bound phosphate at the active site
6P52 · Peptidoglycan D,D-transpeptidase pena: “Crystal structure of transpeptidase domain of PBP2 from neisseria gonorrhoeae with a bound phosphate at the…”. X-ray diffraction, 1 ligand (PO4), 6 pockets (best druggability 0.63). MolNFT v1…
- PDB
- 6P52
- Type
- protein
- Length
- 626 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
- PO4
- Pockets
- 6 · best druggability 0.63
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 | 313 | 37% helix, 19% strand | P08149 |
| B | Peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 313 | 39% helix, 18% strand | P08149 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.63 | 0.78 | 29 | empty |
| 2 | 173 | 0.48 | 0.76 | 27 | PO4 |
| 3 | 50 | 0.45 | 0.85 | 15 | empty |
| 4 | 146 | 0.43 | 0.75 | 26 | empty |
| 5 | 111 | 0.36 | 0.73 | 22 | PO4 |
Interfaces
1 interface between chains.
- A–B · 987 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6P52 · Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae with 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 0.99
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 6P52 · PDBe 6P52 · UniProt P08149
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