MolNFT v1 · #170415 · protein
Structure of pseudomonas aeruginosa penicillin-binding protein 3 (PBP3) in complex with compound 6
6Y6U · Peptidoglycan D,D-transpeptidase ftsi: “Structure of pseudomonas aeruginosa penicillin-binding protein 3 (PBP3) in complex with compound 6”. X-ray diffraction, 1 ligand (ODZ), 3 pockets (best druggability 0.48). MolNFT v1 #170415 on…
- PDB
- 6Y6U
- Type
- protein
- Length
- 493 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
- ODZ
- Pockets
- 3 · best druggability 0.48
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 | 493 | 34% helix, 26% strand | G3XD46 |
Ligands and binding sites
- ODZ · 2-(4-hydroxyphenyl)-~{N}-[(2~{S})-2-methyl-4-oxidanyl-1-oxidanylidene-pent-4-en-2-yl]ethanamide · ligand · chains A
- GOL · Glycerol · additive · 5 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.48 | 0.74 | 32 | empty |
| 2 | 164 | 0.42 | 0.74 | 35 | ODZ |
| 3 | 105 | 0.40 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6Y6U · 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 6Y6U · PDBe 6Y6U · UniProt G3XD46
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