Research workbench
Crystal structure of pseudomonas aeruginosa PBP3 with a R4 substituted vinyl monocarbam
Analyse Crystal structure of pseudomonas aeruginosa PBP3 with a R4 substituted vinyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WEK
- Type
- protein
- Length
- 500 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 3
- UniProt
- K1C6A4
- Ligands
- 3LC
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 3 | protein | 500 | 35% helix, 26% strand | K1C6A4 |
Ligands and binding sites
- 3LC · (3S,4S,7Z)-7-(2-amino-1,3-thiazol-4-yl)-3-ethenyl-4-formyl-1-[({3-(5-hydroxy-4-oxo-3,4-dihydropyridin-2-yl)-4-[3-(methylsulfonyl)propyl]-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl}sulfonyl)amino]-10,10-dimethyl-1,6-dioxo-9-oxa-2,5,8-triazaundec-7-en-11-oic acid · ligand · 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 | 375 | 0.63 | 0.78 | 36 | 3LC |
| 2 | 285 | 0.55 | 0.76 | 45 | empty |
| 3 | 58 | 0.28 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4WEK · Crystal structure of Pseudomonas aeruginosa PBP3 with a R4 substituted vinyl monocarbam · the same entry in another collection · chain A against A, TM-score 1.00
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 K1C6A4
- Elsewhere: RCSB PDB 4WEK · PDBe 4WEK · UniProt K1C6A4
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