MolNFT v1 · #126422 · protein
Crystal structure of vancomycin-ZN(II) complex
5M2K: “Crystal structure of vancomycin-ZN(II) complex”. X-ray diffraction, 3 ligands (RER, BGC, ZN). MolNFT v1 #126422 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M2K
- Type
- protein
- Length
- 14 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vancomycin
- Ligands
- RER, BGC, ZN
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vancomycin | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- RER · vancosamine · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 184 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 glycan (nonstandard, glycosylation).
Compared structures
- 5M2K · Crystal structure of vancomycin-Zn(II) complex · 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
- Elsewhere: RCSB PDB 5M2K · PDBe 5M2K
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