Research workbench
Crystal structure of cel-IV complexed with raffinose
Analyse Crystal structure of cel-IV complexed with raffinose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ALU
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin cel-IV, C-type
- UniProt
- Q7M4F9
- Ligands
- FRU, GLC, GLA, CA
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lectin cel-IV, C-type | protein | 157 | 16% helix, 37% strand | Q7M4F9 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.77 | 0.95 | 20 | empty |
| 2 | 168 | 0.76 | 0.93 | 24 | empty |
| 3 | 265 | 0.72 | 0.86 | 28 | empty |
| 4 | 310 | 0.70 | 0.83 | 34 | empty |
| 5 | 116 | 0.44 | 0.78 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1237 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1195 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 808 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 788 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 238 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 3ALU · Crystal structure of CEL-IV complexed with Raffinose · 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 Q7M4F9
- Elsewhere: RCSB PDB 3ALU · PDBe 3ALU · UniProt Q7M4F9
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