MolNFT v1 · #96150 · protein
Crystal structure of peptidoglycan glycosyltransferase from atopobium parvulum dsm 20469.
4JBF: “Crystal structure of peptidoglycan glycosyltransferase from atopobium parvulum dsm 20469.”. X-ray diffraction, 7 pockets (best druggability 0.75). MolNFT v1 #96150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JBF
- Type
- protein
- Length
- 820 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
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan glycosyltransferase (EC 2.4.1.129) | protein | 410 | 34% helix, 21% strand | C8W8H7 |
| B | Peptidoglycan glycosyltransferase (EC 2.4.1.129) | protein | 410 | 34% helix, 21% strand | C8W8H7 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.75 | 0.82 | 68 | empty |
| 2 | 197 | 0.57 | 0.80 | 39 | empty |
| 3 | 225 | 0.53 | 0.77 | 36 | empty |
| 4 | 60 | 0.47 | 0.84 | 19 | empty |
| 5 | 62 | 0.47 | 0.84 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 562 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 4JBF · Crystal structure of peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469. · 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 4JBF · PDBe 4JBF · UniProt C8W8H7
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