MolNFT v1 · #97042 · protein
Crystal structure of canavalia boliviana lectin in complex with MAN1- 3MAN-ome
4K1Y: “Crystal structure of canavalia boliviana lectin in complex with MAN1- 3MAN-ome”. X-ray diffraction, 5 ligands (MMA, MAN, CD), 3 pockets (best druggability 0.87). MolNFT v1 #97042 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4K1Y
- 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
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Canavalia boliviana lectin | protein | 237 | 3% helix, 47% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.87 | 0.89 | 125 | empty |
| 2 | 51 | 0.27 | 0.75 | 21 | CD |
| 3 | 52 | 0.27 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1228 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1210 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1144 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1097 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4K1Y · Crystal structure of Canavalia boliviana lectin in complex with Man1-3Man-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 4K1Y · PDBe 4K1Y
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