Research workbench
Crystal structure of pa-il lectin complexed with AGAL12BGAL-O-met at 2.4 a resolution
Analyse Crystal structure of pa-il lectin complexed with AGAL12BGAL-O-met at 2.4 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WYF
- Type
- protein
- Length
- 966 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pa-I galactophilic lectin
- UniProt
- Q05097
- Ligands
- MBG, GLA, CA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, H | Pa-I galactophilic lectin | protein | 121 | 2% helix, 45% strand | Q05097 |
| B | Pa-I galactophilic lectin | protein | 119 | 0% helix, 48% strand | Q05097 |
Ligands and binding sites
- MBG · methyl beta-D-galactopyranoside · ligand · 6 copies · chains A, C, D, F, G, H
- GLA · alpha-D-galactopyranose · sugar · 8 copies · chains A, C, D, F, G, H, B, E
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
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 | 1200 | 0.73 | 0.76 | 95 | empty |
| 2 | 709 | 0.72 | 0.79 | 90 | empty |
| 3 | 108 | 0.61 | 0.87 | 24 | empty |
| 4 | 101 | 0.60 | 0.87 | 24 | empty |
| 5 | 94 | 0.53 | 0.84 | 25 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1062 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1046 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 978 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 976 Ų buried · 12 hydrogen bonds · protein-protein
- D–G · 418 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2WYF · Crystal structure of PA-IL lectin complexed with aGal12bGal-O-Met at 2.4 A resolution · the same entry in another collection · chain H against H, TM-score 1.00
- Q05097 · AlphaFold monomer V2.0 prediction for pa-I galactophilic lectin (Q05097) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q05097
- Elsewhere: RCSB PDB 2WYF · PDBe 2WYF · UniProt Q05097
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.