MolNFT v1 · #84888 · protein
Crystal structure of pa-il lectin complexed with GALAG0 at 2.3 a resolution
3ZYB · Pa-I galactophilic lectin: “Crystal structure of pa-il lectin complexed with GALAG0 at 2.3 a resolution”. X-ray diffraction, 4 ligands (PHB, GAL, CA), 10 pockets (best druggability 0.66). MolNFT v1 #84888 on GenesisL1: 3D structure…
- PDB
- 3ZYB
- Type
- protein
- Length
- 977 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pa-I galactophilic lectin; Gala-lys-pro-LEUNH2
- UniProt
- Q05097
- Ligands
- PHB, GAL, CA, NH2
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Pa-I galactophilic lectin | protein | 121 | 2% helix, 45% strand | Q05097 |
| I, J, N | Gala-lys-pro-LEUNH2 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- PHB · P-hydroxybenzoic acid · ligand · 8 copies · chains A, F, I, B, G, J, C, D, E, H, N
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, F, B, G, C, D, E, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- NH2 · Amino group · ion · 3 copies · chains B, I, H, J, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.66 | 0.83 | 44 | empty |
| 2 | 76 | 0.65 | 0.92 | 24 | empty |
| 3 | 236 | 0.62 | 0.82 | 30 | empty |
| 4 | 286 | 0.62 | 0.80 | 48 | CA, GAL, PHB |
| 5 | 206 | 0.62 | 0.82 | 45 | GAL, PHB |
Interfaces
18 interfaces between chains.
- B–C · 1050 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1041 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 188 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 179 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 164 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 3ZYB · Crystal structure of pa-il lectin complexed with GALAG0 at 2.3 a resolution · the same entry in another collection · chain N against N, TM-score 1.00
- Q05097 · AlphaFold monomer V2.0 prediction for pa-I galactophilic lectin (Q05097) · a predicted model of the same protein · chain A 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 3ZYB · PDBe 3ZYB · UniProt Q05097
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