MolNFT v1 · #182080 · protein + DNA
Concanavalin a bound to DNA glycoconjugates, man-tttt and man-aaaa
7MG9 · Concanavalin-a: “Concanavalin a bound to DNA glycoconjugates, man-tttt and man-aaaa”. X-ray diffraction, 4 ligands (SQ0, MAN, MN), 1 pocket (best druggability 0.30). MolNFT v1 #182080 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7MG9
- Type
- protein + DNA
- Length
- 471 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin-a; DNA (5'-D(P*AP*AP*AP*A)-3'); DNA (5'-D(P*TP*TP*TP*T)-3')
- UniProt
- P02866
- Ligands
- SQ0, MAN, MN, CA
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Concanavalin-a | protein | 231 | 3% helix, 46% strand | P02866 |
| B | Concanavalin-a | protein | 232 | 4% helix, 47% strand | P02866 |
| C | DNA (5'-D(P*AP*AP*AP*A)-3') | dna | 4 | — | — |
| D | DNA (5'-D(P*TP*TP*TP*T)-3') | dna | 4 | — | — |
Ligands and binding sites
- SQ0 · 3-{[2-(2-hydroxyethoxy)ethyl]amino}-4-[(6-hydroxyhexyl)amino]cyclobut-3-ene-1,2-dione · ligand · 2 copies · chains A, C, B, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 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 | 0.30 | 0.75 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 963 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 65 Ų buried · 0 hydrogen bonds · protein-nucleic
- B–D · 56 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 P02866
- Elsewhere: RCSB PDB 7MG9 · PDBe 7MG9 · UniProt P02866
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