Research workbench
Crystal structure of pseudomonas aeruginosa lectin 1 complexed with galactose at 1.6 a resolution
Analyse Crystal structure of pseudomonas aeruginosa lectin 1 complexed with galactose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OKO
- Type
- protein
- Length
- 484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pa-I galactophilic lectin
- UniProt
- Q05097
- Ligands
- GAL, GLA, CA, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pa-I galactophilic lectin | protein | 121 | 2% helix, 45% strand | Q05097 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- GLA · alpha-D-galactopyranose · sugar · 3 copies · chains B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.65 | 0.91 | 24 | empty |
| 2 | 58 | 0.64 | 0.93 | 24 | empty |
| 3 | 51 | 0.39 | 0.82 | 18 | empty |
| 4 | 53 | 0.27 | 0.74 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1084 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1073 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 383 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 372 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 243 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1OKO · Crystal structure of Pseudomonas Aeruginosa Lectin 1 complexed with galactose at 1.6 A… · the same entry in another collection · chain A against A, 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 1OKO · PDBe 1OKO · UniProt Q05097
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