MolNFT v1 · #167568 · protein
Crystal structure of pseudomonas aerugonisa PBP3 complexed to gamma- lactam YU253434
6VOT · Peptidoglycan D,D-transpeptidase ftsi: “Crystal structure of pseudomonas aerugonisa PBP3 complexed to gamma- lactam YU253434”. X-ray diffraction, 1 ligand (R7G), 4 pockets (best druggability 0.62). MolNFT v1 #167568 on GenesisL1: 3D…
- PDB
- 6VOT
- Type
- protein
- Length
- 499 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
- Q51504
- Ligands
- R7G
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4) | protein | 499 | 34% helix, 26% strand | Q51504 |
Ligands and binding sites
- R7G · 1-[(2S)-2-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-3-oxopropyl]-4-{[2-(5,6 -dihydroxy-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl]carbamoyl}-2,5-dihydro-1H-pyrazole-3-carboxylic 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 | 379 | 0.62 | 0.78 | 35 | R7G |
| 2 | 216 | 0.52 | 0.76 | 33 | empty |
| 3 | 99 | 0.46 | 0.80 | 19 | empty |
| 4 | 58 | 0.28 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6VOT · Crystal structure of Pseudomonas aerugonisa PBP3 complexed to gamma-lactam YU253434 · 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 Q51504
- Elsewhere: RCSB PDB 6VOT · PDBe 6VOT · UniProt Q51504
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