Research workbench
Galactose-specific lectin from dolichos lablab
Analyse Galactose-specific lectin from dolichos lablab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UK9
- Type
- protein
- Length
- 1,984 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Legume lectin
- Ligands
- CA, MN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Legume lectin | protein | 249 | 3% helix, 47% strand | — |
| B | Legume lectin | protein | 249 | 6% helix, 45% strand | — |
| C, F | Legume lectin | protein | 247 | 4% helix, 47% strand | — |
| D | Legume lectin | protein | 248 | 5% helix, 46% strand | — |
| E, G | Legume lectin | protein | 247 | 3% helix, 45% strand | — |
| H | Legume lectin | protein | 250 | 4% helix, 48% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, C, B, D, E, F, H, G
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C, D, E, G
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.81 | 0.83 | 116 | EDO |
| 2 | 1083 | 0.79 | 0.81 | 156 | EDO |
| 3 | 129 | 0.79 | 0.97 | 45 | EDO |
| 4 | 101 | 0.78 | 0.98 | 24 | EDO |
| 5 | 134 | 0.75 | 0.94 | 27 | EDO |
Interfaces
16 interfaces between chains.
- B–D · 1443 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 1427 Ų buried · 58 hydrogen bonds · protein-protein
- E–G · 1415 Ų buried · 63 hydrogen bonds · protein-protein
- F–H · 1351 Ų buried · 65 hydrogen bonds · protein-protein
- E–F · 1024 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 3UK9 · Galactose-specific lectin from Dolichos lablab · the same entry in another collection · chain G against G, 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 3UK9 · PDBe 3UK9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.