MolNFT v1 · #170418 · protein
Structure of pseudomonas aeruginosa penicillin-binding protein 3 (PBP3) in complex with compound 1
6Y6Z · Peptidoglycan D,D-transpeptidase ftsi: “Structure of pseudomonas aeruginosa penicillin-binding protein 3 (PBP3) in complex with compound 1”. X-ray diffraction, 1 ligand (OEE), 4 pockets (best druggability 0.61). MolNFT v1 #170418 on…
- PDB
- 6Y6Z
- Type
- protein
- Length
- 500 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
- OEE
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 500 | 34% helix, 25% strand | G3XD46 |
Ligands and binding sites
- OEE · ~{tert}-butyl ~{N}-[(2~{S})-2-methyl-4-oxidanyl-1-oxidanylidene-pent-4-en-2-yl]carbamate · ligand · chains A
- GOL · Glycerol · additive · 3 copies · 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 | 0.61 | 0.79 | 34 | OEE |
| 2 | 149 | 0.40 | 0.73 | 20 | empty |
| 3 | 132 | 0.40 | 0.75 | 19 | empty |
| 4 | 104 | 0.40 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6Y6Z · Structure of Pseudomonas aeruginosa Penicillin-Binding Protein 3 (PBP3) in complex with… · 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 6Y6Z · PDBe 6Y6Z · UniProt G3XD46
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