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Bifunctional dendrimers
Analyse Bifunctional dendrimers in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D2A
- Type
- protein
- Length
- 240 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin; Zdc-ala-pro-ala-lys-phe-cys-ala-pro-ala-phb-gal
- UniProt
- A0A069Q9V4
- Ligands
- PHB, ZDC, GAL, CA
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fucose-binding lectin | protein | 114 | 0% helix, 70% strand | A0A069Q9V4 |
| C | Zdc-ala-pro-ala-lys-phe-cys-ala-pro-ala-phb-gal | protein | 6 | 0% helix, 0% strand | — |
| D, E | Zdc-ala-pro-ala-lys-phe-cys-ala-pro-ala-phb-gal | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- PHB · P-hydroxybenzoic acid · ligand · chains C
- ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 2 copies · chains A, B, D, E
- GAL · beta-D-galactopyranose · sugar
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.29 | 0.75 | 22 | ZDC |
Interfaces
5 interfaces between chains.
- A–B · 1335 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 131 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 88 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 86 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 63 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan, 1 covalent, 1 isopeptide (glycosylation, covalent ligand, isopeptide).
Compared structures
- 5D2A · Bifunctional dendrimers · 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 A0A069Q9V4
- Elsewhere: RCSB PDB 5D2A · PDBe 5D2A · UniProt A0A069Q9V4
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