Research workbench
Concanavalin from canavalia brasiliensis
Analyse Concanavalin from canavalia brasiliensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AZD
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conbr
- UniProt
- P55915
- Ligands
- CA, MN
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Conbr | protein | 237 | 4% helix, 44% strand | P55915 |
Ligands and binding sites
- 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.87 | 0.88 | 92 | empty |
| 2 | 50 | 0.68 | 0.97 | 16 | empty |
| 3 | 175 | 0.61 | 0.84 | 36 | empty |
| 4 | 204 | 0.61 | 0.82 | 36 | empty |
| 5 | 173 | 0.60 | 0.83 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1216 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1200 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1057 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1042 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 61 Ų buried · 3 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 P55915
- Elsewhere: RCSB PDB 1AZD · PDBe 1AZD · UniProt P55915
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