Research workbench
X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair
Analyse X-ray structure of a lectin-bound DNA duplex containing an unnatural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HCH
- Type
- protein + DNA
- Length
- 140 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin; DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3'); DNA…
- UniProt
- A0A069Q9V4
- Ligands
- 61J, CA, NA
- Pockets
- 1 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 71% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fucose-binding lectin | protein | 114 | 0% helix, 71% strand | A0A069Q9V4 |
| B | DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3') | dna | 13 | — | — |
| E | DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3') | dna | 13 | — | — |
Ligands and binding sites
- 61J · (6S)-2,6-anhydro-1-deoxy-6-(2-{[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]oxy}ethyl)-D-galactitol · ligand · chains A, B, E
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal
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 | 102 | 0.41 | 0.78 | 18 | CA, 61J |
Interfaces
3 interfaces between chains.
- B–E · 698 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–B · 87 Ų buried · 0 hydrogen bonds · protein-nucleic
- A–E · 59 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 5HCH · X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair · 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 5HCH · PDBe 5HCH · UniProt A0A069Q9V4
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