MolNFT v1 · #69182 · protein
The crystal structures of two fragments truncated from 5-bladed beta- propeller lectin, tachylectin-2 (LIB1-B7-18 and LIB2-D2-15)
3KIF · 5-bladed beta-propeller lectin: “The crystal structures of two fragments truncated from 5-bladed beta- propeller lectin, tachylectin-2…”. X-ray diffraction, 2 ligands (GDL, SO4), 5 pockets (best druggability 0.85). MolNFT v1 #69182…
- PDB
- 3KIF
- Type
- protein
- Length
- 902 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-bladed beta-propeller lectin
- Ligands
- GDL, SO4
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-bladed beta-propeller lectin | protein | 93 | 15% helix, 39% strand | — |
| B, G | 5-bladed beta-propeller lectin | protein | 88 | 8% helix, 42% strand | — |
| C, H | 5-bladed beta-propeller lectin | protein | 85 | 11% helix, 41% strand | — |
| D | 5-bladed beta-propeller lectin | protein | 91 | 11% helix, 44% strand | — |
| E, J | 5-bladed beta-propeller lectin | protein | 93 | 15% helix, 39% strand | — |
| F | 5-bladed beta-propeller lectin | protein | 92 | 14% helix, 39% strand | — |
| I | 5-bladed beta-propeller lectin | protein | 94 | 17% helix, 38% strand | — |
Ligands and binding sites
- GDL · 2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone · ligand · 9 copies · chains A, B, C, D, E, F, G, I, J
- SO4 · Sulfate ion · ion · 2 copies · chains E, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.85 | 0.86 | 88 | empty |
| 2 | 1015 | 0.81 | 0.82 | 92 | empty |
| 3 | 502 | 0.78 | 0.85 | 35 | empty |
| 4 | 529 | 0.78 | 0.84 | 35 | empty |
| 5 | 326 | 0.56 | 0.75 | 34 | empty |
Interfaces
21 interfaces between chains.
- H–J · 1311 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 1291 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 1150 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1119 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1088 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3KIF · The crystal structures of two fragments truncated from 5-bladed beta-propeller lectin… · 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
- Elsewhere: RCSB PDB 3KIF · PDBe 3KIF
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