Research workbench
Peanut lectin complexed with N-beta-D-galactopyranosyl-L-succinamoyl derivative (ngs)
Analyse Peanut lectin complexed with N-beta-D-galactopyranosyl-L-succinamoyl derivative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VAW
- Type
- protein
- Length
- 928 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose-binding lectin
- UniProt
- P02872
- Ligands
- S3W, MN, CA
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Galactose-binding lectin | protein | 232 | 4% helix, 50% strand | P02872 |
Ligands and binding sites
- S3W · N-[(2R,3R,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl) tetrahydro-2H-pyran-2-yl]-N'-[(1-{[(2R,3S,4S,5R,6S)-3, 4,5-trihydroxy-6-methoxytetrahydro-2H-pyran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]butanediamide · ligand · 4 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
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.76 | 0.81 | 99 | empty |
| 2 | 175 | 0.46 | 0.75 | 34 | empty |
| 3 | 168 | 0.45 | 0.75 | 27 | empty |
| 4 | 155 | 0.45 | 0.76 | 28 | empty |
| 5 | 132 | 0.43 | 0.76 | 32 | empty |
Interfaces
6 interfaces between chains.
- B–C · 987 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 981 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 661 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 597 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 60 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6VAW · Peanut lectin complexed with N-beta-D-galactopyranosyl-L-succinamoyl derivative (NGS) · the same entry in another collection · chain A against A, TM-score 1.00
- P02872 · AlphaFold monomer V2.0 prediction for galactose-binding lectin (P02872) · a predicted model of the same protein · 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
- Every structure of UniProt P02872
- Elsewhere: RCSB PDB 6VAW · PDBe 6VAW · UniProt P02872
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