Research workbench
Crystal structure of hemolytic lectin cel-III complexed with galnac
Analyse Crystal structure of hemolytic lectin cel-III complexed with galnac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z48
- Type
- protein
- Length
- 862 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemolytic lectin cel-III
- UniProt
- Q868M7
- Ligands
- NGA, A2G, CA, MG
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemolytic lectin cel-III | protein | 431 | 11% helix, 41% strand | Q868M7 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 8 copies · chains A, B
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 10 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.74 | 0.81 | 77 | NGA |
| 2 | 671 | 0.74 | 0.81 | 78 | NGA |
| 3 | 235 | 0.66 | 0.84 | 27 | empty |
| 4 | 255 | 0.66 | 0.83 | 26 | empty |
| 5 | 230 | 0.64 | 0.83 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 2Z48 · Crystal Structure of Hemolytic Lectin CEL-III Complexed with GalNac · 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 Q868M7
- Elsewhere: RCSB PDB 2Z48 · PDBe 2Z48 · UniProt Q868M7
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