Research workbench
A transient unlocked concanavalin a structure with MN2+ bound in the transition metal ion binding site S1 and an empty calcium binding site S2
Analyse A transient unlocked concanavalin a structure with MN2+ bound in the transition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DQ4
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin-br
- UniProt
- P55915
- Ligands
- MN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Concanavalin-br | protein | 226 | 3% helix, 50% strand | P55915 |
| B | Concanavalin-br | protein | 223 | 3% helix, 50% strand | P55915 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
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 | 56 | 0.72 | 0.98 | 16 | empty |
| 2 | 57 | 0.68 | 0.96 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1210 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1DQ4 · A transient unlocked concanavalin A structure with MN2+ bound in the transition metal ion… · the same entry in another collection · chain A against A, TM-score 1.00
- P55915 · AlphaFold monomer V2.0 prediction for concanavalin-br (P55915) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P55915
- Elsewhere: RCSB PDB 1DQ4 · PDBe 1DQ4 · UniProt P55915
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