Research workbench
Nitrocefin reacted with catalytic serine (SER294) of penicillin- binding protein 3 from pseudomonas aeruginosa
Analyse Nitrocefin reacted with catalytic serine (SER294) of penicillin- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HR6
- Type
- protein
- Length
- 492 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
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 492 | 33% helix, 21% strand | G3XD46 |
Ligands and binding sites
- NEF · Nitrocefin - open form · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.58 | 0.77 | 41 | empty |
| 2 | 214 | 0.49 | 0.76 | 35 | NEF |
| 3 | 115 | 0.45 | 0.78 | 18 | empty |
| 4 | 58 | 0.28 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6HR6 · Nitrocefin reacted with catalytic serine (Ser294) of penicillin-binding protein 3 from… · 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 6HR6 · PDBe 6HR6 · UniProt G3XD46
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