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Crystal structure of a lectin from canavalia maritima seeds (cml) in complex with MAN1-3MAN-ome
Analyse Crystal structure of a lectin from canavalia maritima seeds (cml) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P37
- Type
- protein
- Length
- 933 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin a
- UniProt
- P81364
- Ligands
- ZEL, MAN, MN, CA
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Concanavalin a | protein | 234 | 4% helix, 45% strand | P81364 |
| B | Concanavalin a | protein | 234 | 4% helix, 47% strand | P81364 |
| C | Concanavalin a | protein | 232 | 4% helix, 46% strand | P81364 |
| D | Concanavalin a | protein | 233 | 4% helix, 46% strand | P81364 |
Ligands and binding sites
- ZEL · methyl beta-D-altropyranoside · ligand · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 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
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 | 1023 | 0.84 | 0.85 | 107 | empty |
| 2 | 50 | 0.36 | 0.80 | 14 | empty |
| 3 | 54 | 0.35 | 0.79 | 20 | empty |
| 4 | 52 | 0.29 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1056 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1030 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 872 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 818 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2P37 · Crystal structure of a lectin from Canavalia maritima seeds (CML) in complex with… · 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
- Every structure of UniProt P81364
- Elsewhere: RCSB PDB 2P37 · PDBe 2P37 · UniProt P81364
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