MolNFT v1 · #107062 · protein
Crystal structure of canavalia maritima lectin (conm) complexed with a dinucleotide
4TYS · Concanavalin-a: “Crystal structure of canavalia maritima lectin (conm) complexed with a dinucleotide”. X-ray diffraction, 1 ligand (3XZ), 9 pockets (best druggability 0.83). MolNFT v1 #107062 on GenesisL1: 3D structure, binding…
- PDB
- 4TYS
- Type
- protein
- Length
- 1,393 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin-a
- UniProt
- P81460
- Ligands
- 3XZ
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Concanavalin-a | protein | 232 | 3% helix, 44% strand | P81460 |
| C | Concanavalin-a | protein | 233 | 0% helix, 44% strand | P81460 |
Ligands and binding sites
- 3XZ · bis{[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxytetrahydrofuran-2-yl]methyl} hydrogen phosphate · ligand · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.83 | 0.85 | 92 | 3XZ |
| 2 | 57 | 0.71 | 0.98 | 20 | empty |
| 3 | 422 | 0.65 | 0.79 | 50 | empty |
| 4 | 358 | 0.65 | 0.80 | 52 | empty |
| 5 | 70 | 0.53 | 0.86 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–E · 1084 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 972 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 823 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 822 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 319 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4TYS · Crystal structure of Canavalia maritima lectin (ConM) complexed with a dinucleotide · the same entry in another collection · chain F against F, TM-score 1.00
- P81460 · AlphaFold monomer V2.0 prediction for concanavalin-a (P81460) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P81460
- Elsewhere: RCSB PDB 4TYS · PDBe 4TYS · UniProt P81460
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