Research workbench
Structure of lectin from the sea mussel crenomytilus grayanus
Analyse Structure of lectin from the sea mussel crenomytilus grayanus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DUY
- Type
- protein
- Length
- 899 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GALNAC/GAL-specific lectin
- UniProt
- H2FH31
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | GALNAC/GAL-specific lectin | protein | 150 | 6% helix, 43% strand | H2FH31 |
| D | GALNAC/GAL-specific lectin | protein | 149 | 6% helix, 43% strand | H2FH31 |
Ligands and binding sites
- GOL · Glycerol · additive · 18 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.73 | 0.76 | 98 | GOL |
| 2 | 224 | 0.54 | 0.78 | 38 | GOL |
| 3 | 53 | 0.50 | 0.87 | 17 | GOL |
| 4 | 131 | 0.42 | 0.76 | 22 | GOL |
| 5 | 68 | 0.32 | 0.75 | 13 | empty |
Interfaces
7 interfaces between chains.
- E–F · 330 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 323 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 319 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 316 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 188 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DUY · Structure of lectin from the sea mussel Crenomytilus grayanus · 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 H2FH31
- Elsewhere: RCSB PDB 5DUY · PDBe 5DUY · UniProt H2FH31
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