Research workbench
Crystal structure of the transpeptidase domain of neisseria gonorrhoeae penicillin-binding protein 2 derived from the penicillin- resistant strain 6140
Analyse Crystal structure of the transpeptidase domain of neisseria gonorrhoeae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U3T
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2
- EC
- 3.4.16.4
- UniProt
- P08149
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2 (EC 3.4.16.4) | protein | 322 | 36% helix, 22% strand | P08149 |
| B | Penicillin-binding protein 2 (EC 3.4.16.4) | protein | 314 | 36% helix, 21% strand | P08149 |
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 | 370 | 0.61 | 0.77 | 28 | empty |
| 2 | 153 | 0.45 | 0.76 | 27 | empty |
| 3 | 74 | 0.45 | 0.82 | 19 | empty |
| 4 | 141 | 0.43 | 0.75 | 27 | empty |
| 5 | 117 | 0.39 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 926 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4U3T · Crystal structure of the transpeptidase domain of Neisseria gonorrhoeae… · 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 0.98
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 4U3T · PDBe 4U3T · UniProt P08149
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