Research workbench
Co-crystals of demetallized concanavalin a with zinc having a zinc ion bound in the S1 site
Analyse Co-crystals of demetallized concanavalin a with zinc having a zinc ion bound in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ENQ
- Type
- protein
- Length
- 916 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin a
- UniProt
- P02866
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Concanavalin a | protein | 230 | 4% helix, 49% strand | P02866 |
| B | Concanavalin a | protein | 232 | 3% helix, 50% strand | P02866 |
| C | Concanavalin a | protein | 230 | 3% helix, 50% strand | P02866 |
| D | Concanavalin a | protein | 224 | 3% helix, 51% strand | P02866 |
Ligands and binding sites
- ZN · Zinc 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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.76 | 0.92 | 40 | empty |
| 2 | 226 | 0.75 | 0.90 | 38 | empty |
| 3 | 284 | 0.73 | 0.87 | 44 | empty |
| 4 | 249 | 0.70 | 0.86 | 41 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1178 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1153 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1144 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1138 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1ENQ · Co-crystals of demetallized concanavalin a with zinc having a zinc ion bound in the S1… · the same entry in another collection · chain D against D, TM-score 1.00
- P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain A against A, TM-score 0.51
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 1ENQ · PDBe 1ENQ · UniProt P02866
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