Research workbench
Crystal structure of concanavalin a bound to an octa-alpha-mannosyl- octasilsesquioxane cluster
Analyse Crystal structure of concanavalin a bound to an octa-alpha-mannosyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QLQ
- Type
- protein
- Length
- 939 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin-a
- UniProt
- P81461
- Ligands
- MAN, CA, MN
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Concanavalin-a | protein | 236 | 5% helix, 46% strand | P81461 |
| B | Concanavalin-a | protein | 235 | 5% helix, 46% strand | P81461 |
| D | Concanavalin-a | protein | 232 | 5% helix, 45% strand | P81461 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.85 | 0.86 | 109 | empty |
| 2 | 90 | 0.52 | 0.84 | 27 | empty |
| 3 | 68 | 0.36 | 0.78 | 21 | empty |
| 4 | 65 | 0.31 | 0.75 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1141 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1098 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 858 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 785 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3QLQ · Crystal structure of Concanavalin A bound to an octa-alpha-mannosyl-octasilsesquioxane… · the same entry in another collection · chain B against B, TM-score 1.00
- P81461 · AlphaFold monomer V2.0 prediction for concanavalin-a (P81461) · a predicted model of the same protein · chain D 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 P81461
- Elsewhere: RCSB PDB 3QLQ · PDBe 3QLQ · UniProt P81461
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