Research workbench
Crystal structure of canavalia boliviana lectin in complex with MAN1- 4MAN-ome
Analyse Crystal structure of canavalia boliviana lectin in complex with MAN1- 4MAN-ome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K1Z
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Canavalia boliviana lectin
- Ligands
- MMA, MAN, CD, MN, CA, CL
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Canavalia boliviana lectin | protein | 237 | 5% helix, 46% strand | — |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · sugar · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- CD · Cadmium ion · metal · 9 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
- CL · Chloride ion · ion · 2 copies · chains B, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.87 | 0.89 | 138 | empty |
| 2 | 82 | 0.43 | 0.80 | 24 | empty |
| 3 | 62 | 0.43 | 0.81 | 20 | empty |
| 4 | 89 | 0.33 | 0.74 | 24 | CD |
Interfaces
6 interfaces between chains.
- C–D · 1224 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1198 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1175 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 1159 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4K1Z · Crystal structure of Canavalia boliviana lectin in complex with Man1-4Man-OMe · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 4K1Z · PDBe 4K1Z
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