Research workbench
New strategy to analyze structures of glycopeptide antibiotic-target complexes
Analyse New strategy to analyze structures of glycopeptide antibiotic-target complexes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RUN
- Type
- protein
- Length
- 175 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme; Vancomycin
- EC
- 3.2.1.17
- UniProt
- P00720
- Ligands
- RER, BGC, PO4, CL
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 168 | 63% helix, 10% strand | P00720 |
| B | Vancomycin | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- RER · vancosamine · ligand · chains B
- BGC · beta-D-glucopyranose · sugar · chains A, B
- PO4 · Phosphate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.52 | 0.75 | 32 | TRS |
| 2 | 66 | 0.39 | 0.79 | 15 | MRD |
Interfaces
1 interface between chains.
- A–B · 497 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified, 2 d-amino, 1 glycan (nonstandard, D-amino acid, glycosylation).
Compared structures
- 3RUN · New strategy to analyze structures of glycopeptide antibiotic-target complexes · 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 P00720
- Elsewhere: RCSB PDB 3RUN · PDBe 3RUN · UniProt P00720
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