Research workbench
X-ray crystal structure of a pea lectin-trimannoside complex at 2.6 ångströms resolution
Analyse X-ray crystal structure of a pea lectin-trimannoside complex at 2.6 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RIN
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pea lectin
- UniProt
- P02867
- Ligands
- MAN, MN, CA
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pea lectin | protein | 180 | 3% helix, 46% strand | P02867 |
| B | Pea lectin | protein | 47 | 9% helix, 64% strand | P02867 |
| D | Pea lectin | protein | 49 | 8% helix, 61% strand | P02867 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 2 copies · chains A, C
- CA · Calcium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.47 | 0.79 | 20 | empty |
| 2 | 90 | 0.42 | 0.79 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3927 Ų buried · 102 hydrogen bonds · protein-protein
- A–B · 3870 Ų buried · 99 hydrogen bonds · protein-protein
- A–C · 893 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 135 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 134 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1RIN · X-ray crystal structure of a pea lectin-trimannoside complex at 2.6 ångströms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P02867 · AlphaFold monomer V2.0 prediction for lectin (P02867) · a predicted model of the same protein · chain A 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 P02867
- Elsewhere: RCSB PDB 1RIN · PDBe 1RIN · UniProt P02867
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