MolNFT v1 · #102528 · protein
Crystal structure of PBP3 in complex with compound 14 ((2E)-2-({[(2S)- 2-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(1,5-dihydroxy-4-oxo-1,4- dihydropyridin-2-YL)METHOXY]IMINO}ACETYL]AMINO}-3- OXOPROPYL]OXY}IMINO)PENTANEDIOIC acid)
4OOL · Cell division protein ftsi [peptidoglycan synthetase]: “Crystal structure of PBP3 in complex with compound 14 ((2E)-2-({[(2S)…”. X-ray diffraction, 1 ligand (2U2), 4 pockets (best druggability 0.63). MolNFT v1 #102528 on GenesisL1…
- PDB
- 4OOL
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein ftsi [peptidoglycan synthetase]
- EC
- 2.4.1.129
- UniProt
- U6AVY0
- Ligands
- 2U2
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein ftsi [peptidoglycan synthetase] (EC 2.4.1.129) | protein | 499 | 35% helix, 25% strand | U6AVY0 |
Ligands and binding sites
- 2U2 · (2E)-2-({[(2S)-2-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)methoxy]imino}acetyl]amino}-3-oxopropyl]oxy}imino)pentanedioic acid · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.63 | 0.79 | 37 | 2U2 |
| 2 | 209 | 0.52 | 0.77 | 32 | empty |
| 3 | 91 | 0.39 | 0.77 | 19 | empty |
| 4 | 52 | 0.26 | 0.73 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4OOL · Crystal structure of PBP3 in complex with compound 14… · 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 U6AVY0
- Elsewhere: RCSB PDB 4OOL · PDBe 4OOL · UniProt U6AVY0
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