MolNFT v1 · #159914 · protein
Crystal structure of the transpeptidase domain of PBP2 from neisseria gonorrhoeae in apo form
6P53 · Peptidoglycan D,D-transpeptidase pena: “Crystal structure of the transpeptidase domain of PBP2 from neisseria gonorrhoeae in apo form”. X-ray diffraction, 1 ligand (PO4), 6 pockets (best druggability 0.62). MolNFT v1 #159914 on…
- PDB
- 6P53
- Type
- protein
- Length
- 640 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 0.62
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 315 | 37% helix, 20% strand | P08149 |
| B | Peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4) | protein | 325 | 37% helix, 22% strand | P08149 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains 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 | 384 | 0.62 | 0.77 | 27 | empty |
| 2 | 69 | 0.44 | 0.82 | 19 | empty |
| 3 | 143 | 0.42 | 0.75 | 22 | empty |
| 4 | 132 | 0.41 | 0.74 | 25 | empty |
| 5 | 127 | 0.40 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 975 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6P53 · Crystal structure of the transpeptidase domain of PBP2 from Neisseria gonorrhoeae in apo… · 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 6P53 · PDBe 6P53 · UniProt P08149
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