Research workbench
Structure of a putative peptidoglycan glycosyltransferase from atopobium parvulum in complex with cephalothin
Analyse Structure of a putative peptidoglycan glycosyltransferase from atopobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R0Q
- Type
- protein
- Length
- 825 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
- CEP, SCN
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan glycosyltransferase (EC 2.4.1.129) | protein | 413 | 33% helix, 25% strand | C8W8H7 |
| B | Peptidoglycan glycosyltransferase (EC 2.4.1.129) | protein | 412 | 33% helix, 25% strand | C8W8H7 |
Ligands and binding sites
- CEP · Cephalothin group · ligand · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · 2 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.73 | 0.79 | 68 | CEP |
| 2 | 249 | 0.58 | 0.79 | 30 | empty |
| 3 | 233 | 0.54 | 0.77 | 32 | CEP |
| 4 | 62 | 0.52 | 0.87 | 19 | empty |
| 5 | 53 | 0.49 | 0.87 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 542 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 4R0Q · 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 4R0Q · PDBe 4R0Q · UniProt C8W8H7
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