Research workbench
Multivalency effects in glycopeptide dendrimer inhibitors of pseudomonas aeruginosa biofilms targeting lectin leca
Analyse Multivalency effects in glycopeptide dendrimer inhibitors of pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D21
- Type
- protein
- Length
- 484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leca
- UniProt
- A0A073A1F3
- Ligands
- 56N, CA
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Leca | protein | 121 | 2% helix, 49% strand | A0A073A1F3 |
Ligands and binding sites
- 56N · phenyl beta-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.64 | 0.93 | 24 | empty |
| 2 | 59 | 0.62 | 0.92 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1070 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1047 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 364 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 361 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 263 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5D21 · Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas aeruginosa… · 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 A0A073A1F3
- Elsewhere: RCSB PDB 5D21 · PDBe 5D21 · UniProt A0A073A1F3
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