Research workbench
Crystal structure of jacalin-T-antigen complex
Analyse Crystal structure of jacalin-T-antigen complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M26
- Type
- protein
- Length
- 594 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jacalin, alpha chain; Jacalin, beta chain
- Ligands
- A2G, GAL
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Jacalin, alpha chain | protein | 133 | 0% helix, 67% strand | — |
| B, F, H | Jacalin, beta chain | protein | 15 | 0% helix, 47% strand | — |
| D | Jacalin, beta chain | protein | 17 | 0% helix, 41% strand | — |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, C, E, G
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.81 | 0.87 | 83 | empty |
| 2 | 242 | 0.50 | 0.75 | 38 | empty |
| 3 | 147 | 0.39 | 0.73 | 28 | empty |
| 4 | 60 | 0.29 | 0.74 | 16 | empty |
Interfaces
22 interfaces between chains.
- C–D · 559 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 540 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 534 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 528 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 464 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1M26 · Crystal structure of jacalin-T-antigen complex · the same entry in another collection · chain H against H, 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 1M26 · PDBe 1M26
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