Research workbench
High resolution structure of galactose binding lectin from champedak (cgb)
Analyse High resolution structure of galactose binding lectin from champedak (cgb) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AK4
- Type
- protein
- Length
- 1,191 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agglutinin alpha chain; Agglutinin beta-4 chain
- UniProt
- P18670, Q9S8T0
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | Agglutinin alpha chain | protein | 133 | 0% helix, 67% strand | P18670 |
| B, F, L, N, P | Agglutinin beta-4 chain | protein | 16 | 0% helix, 44% strand | Q9S8T0 |
| D, H | Agglutinin beta-4 chain | protein | 15 | 0% helix, 47% strand | Q9S8T0 |
| J | Agglutinin beta-4 chain | protein | 17 | 0% helix, 41% strand | Q9S8T0 |
Ligands and binding sites
- P6G · Hexaethylene glycol · additive · 6 copies · chains A, C, E, M, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.87 | 0.88 | 144 | empty |
| 2 | 550 | 0.70 | 0.79 | 62 | empty |
| 3 | 555 | 0.64 | 0.75 | 60 | empty |
| 4 | 150 | 0.55 | 0.81 | 30 | empty |
| 5 | 115 | 0.41 | 0.76 | 21 | empty |
Interfaces
45 interfaces between chains.
- I–J · 583 Ų buried · 8 hydrogen bonds · protein-protein
- K–L · 580 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 572 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 555 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 552 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4AK4 · High resolution structure of Galactose Binding lectin from Champedak (CGB) · the same entry in another collection · chain P against P, 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 P18670
- Every structure of UniProt Q9S8T0
- Elsewhere: RCSB PDB 4AK4 · PDBe 4AK4 · UniProt P18670 · UniProt Q9S8T0
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