Research workbench
Concanavalin a bound to a DNA glycoconjugate, A(MAN-T)AT
Analyse Concanavalin a bound to a DNA glycoconjugate, A(MAN-T)AT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MGB
- Type
- protein
- Length
- 928 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin-a
- UniProt
- P02866
- Ligands
- MMA, MN, CA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Concanavalin-a | protein | 232 | 5% helix, 44% strand | P02866 |
| B | Concanavalin-a | protein | 233 | 5% helix, 45% strand | P02866 |
| C | Concanavalin-a | protein | 231 | 5% helix, 46% strand | P02866 |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · sugar · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.74 | 0.78 | 76 | empty |
| 2 | 518 | 0.70 | 0.80 | 76 | empty |
| 3 | 536 | 0.69 | 0.79 | 71 | empty |
| 4 | 142 | 0.55 | 0.82 | 25 | empty |
| 5 | 69 | 0.41 | 0.80 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–C · 703 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 616 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 328 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
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 7MGB · PDBe 7MGB · UniProt P02866
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