MolNFT v1 · #105621 · protein
Structure of a putative peptidoglycan glycosyltransferase from atopobium parvulum in complex with nafcillin
4RA7: “Structure of a putative peptidoglycan glycosyltransferase from atopobium parvulum in complex with nafcillin”. X-ray diffraction, 1 ligand (NXU), 8 pockets (best druggability 0.74). MolNFT v1 #105621 on GenesisL1: 3D structure…
- PDB
- 4RA7
- Type
- protein
- Length
- 832 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
- NXU
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan glycosyltransferase (EC 2.4.1.129) | protein | 416 | 35% helix, 24% strand | C8W8H7 |
| B | Peptidoglycan glycosyltransferase (EC 2.4.1.129) | protein | 416 | 34% helix, 24% strand | C8W8H7 |
Ligands and binding sites
- NXU · (2R,4S)-2-[(1R)-2-hydroxy-1-{[(2-hydroxynaphthalen-1-yl)carbonyl]amino}ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.74 | 0.78 | 84 | NXU |
| 2 | 263 | 0.57 | 0.78 | 35 | empty |
| 3 | 90 | 0.56 | 0.85 | 21 | empty |
| 4 | 67 | 0.47 | 0.84 | 19 | empty |
| 5 | 62 | 0.46 | 0.84 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 591 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 4RA7 · 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 4RA7 · PDBe 4RA7 · UniProt C8W8H7
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