Research workbench
Nitrocefin acylation of both catalytic serines of the Y409 mutant of penicillin-binding protein 3 from P. aeruginosa
Analyse Nitrocefin acylation of both catalytic serines of the Y409 mutant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HR9
- Type
- protein
- Length
- 491 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan D,D-transpeptidase ftsi
- EC
- 3.4.16.4
- UniProt
- G3XD46
- Ligands
- NEF
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 491 | 33% helix, 24% strand | G3XD46 |
Ligands and binding sites
- NEF · Nitrocefin - open form · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.61 | 0.76 | 51 | empty |
| 2 | 176 | 0.56 | 0.80 | 21 | NEF |
| 3 | 92 | 0.33 | 0.73 | 19 | NEF |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6HR9 · Nitrocefin acylation of both catalytic serines of the Y409 mutant of penicillin-binding… · the same entry in another collection · chain A against A, TM-score 1.00
- G3XD46 · AlphaFold monomer V2.0 prediction for peptidoglycan D,D-transpeptidase ftsi (G3XD46) · 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 G3XD46
- Elsewhere: RCSB PDB 6HR9 · PDBe 6HR9 · UniProt G3XD46
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