Research workbench
Crystal structure of the lectin pa-il from pseudomonas aeruginoas in complex with melibiose
Analyse Crystal structure of the lectin pa-il from pseudomonas aeruginoas in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AL9
- Type
- protein
- Length
- 968 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pa-I galactophilic lectin
- UniProt
- Q05097
- Ligands
- GLA, GLC, CA
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 45% 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 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 8 copies · chains F, H, A, B, C, D, E, G
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains F, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 5 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
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.77 | 0.84 | 64 | empty |
| 2 | 57 | 0.68 | 0.96 | 24 | EDO |
| 3 | 71 | 0.66 | 0.93 | 24 | EDO |
| 4 | 96 | 0.62 | 0.88 | 24 | EDO |
| 5 | 193 | 0.61 | 0.82 | 26 | empty |
Interfaces
16 interfaces between chains.
- E–F · 1107 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1086 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1068 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 381 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4AL9 · Crystal structure of the lectin PA-IL from Pseudomonas aeruginoas in complex with… · 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 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 4AL9 · PDBe 4AL9 · UniProt Q05097
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