Research workbench
Crystal structure of cel-IV complexed with melibiose
Analyse Crystal structure of cel-IV complexed with melibiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ALT
- Type
- protein
- Length
- 624 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin cel-IV, C-type
- UniProt
- Q7M4F9
- Ligands
- GLC, GLA, CA
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lectin cel-IV, C-type | protein | 156 | 14% helix, 38% strand | Q7M4F9 |
Ligands and binding sites
- 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.77 | 0.95 | 20 | empty |
| 2 | 174 | 0.74 | 0.91 | 26 | empty |
| 3 | 580 | 0.73 | 0.80 | 49 | empty |
| 4 | 93 | 0.46 | 0.80 | 24 | empty |
| 5 | 101 | 0.45 | 0.79 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1221 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1212 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 795 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 756 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 83 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3ALT · Crystal structure of CEL-IV complexed with Melibiose · the same entry in another collection · chain D against D, 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 3ALT · PDBe 3ALT · UniProt Q7M4F9
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