MolNFT v1 · #105389 · protein
Structure of a putative peptidoglycan glycosyltransferase from atopobium parvulum in complex with cefapirin
4R3J: “Structure of a putative peptidoglycan glycosyltransferase from atopobium parvulum in complex with cefapirin”. X-ray diffraction, 2 ligands (CFU, PO4), 8 pockets (best druggability 0.54). MolNFT v1 #105389 on GenesisL1: 3D structure…
- PDB
- 4R3J
- Type
- protein
- Length
- 814 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan glycosyltransferase
- EC
- 2.4.1.129
- UniProt
- C8W8H7
- Ligands
- CFU, PO4
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan glycosyltransferase (EC 2.4.1.129) | protein | 407 | 36% helix, 24% strand | C8W8H7 |
| B | Peptidoglycan glycosyltransferase (EC 2.4.1.129) | protein | 407 | 35% helix, 24% strand | C8W8H7 |
Ligands and binding sites
- CFU · (2R)-2-[(1R)-1-(acetylamino)-2-oxoethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.54 | 0.76 | 34 | empty |
| 2 | 223 | 0.53 | 0.77 | 35 | CFU |
| 3 | 181 | 0.52 | 0.78 | 27 | CFU |
| 4 | 226 | 0.51 | 0.76 | 26 | empty |
| 5 | 106 | 0.41 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 575 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 4R3J · Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in… · 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 C8W8H7
- Elsewhere: RCSB PDB 4R3J · PDBe 4R3J · UniProt C8W8H7
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