Research workbench
Crystal structure of the transpeptidase domain of PBP2 from neisseria gonorrhoeae in apo form
Analyse Crystal structure of the transpeptidase domain of PBP2 from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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