Research workbench
Crystal structure of tp domain from escherichia COLI penicillin- binding protein 3 in complex with penicillin
Analyse Crystal structure of tp domain from escherichia COLI penicillin- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I1I
- Type
- protein
- Length
- 322 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan D,D-transpeptidase FTSI,PEPTIDOGLYCAN D,D- transpeptidase ftsi
- EC
- 3.4.16.4
- UniProt
- P0AD69
- Ligands
- JPP
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase FTSI,PEPTIDOGLYCAN D,D- transpeptidase ftsi (EC 3.4.16.4) | protein | 322 | 35% helix, 22% strand | P0AD69 |
Ligands and binding sites
- JPP · Piperacillin (Open Form) · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.57 | 0.77 | 35 | JPP |
| 2 | 59 | 0.31 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6I1I · Crystal structure of TP domain from Escherichia coli penicillin-binding protein 3 in… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AD69 · AlphaFold monomer V2.0 prediction for peptidoglycan D,D-transpeptidase ftsi (P0AD69) · a predicted model of the same protein · chain A 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 P0AD69
- Elsewhere: RCSB PDB 6I1I · PDBe 6I1I · UniProt P0AD69
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