Research workbench
Crystal structure of the liprin-alpha3_SAM123/LAR_D1D2 complex
Analyse Crystal structure of the liprin-alpha3_SAM123/LAR_D1D2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KR4
- Type
- protein
- Length
- 3,065 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- Homo sapiens; Mus musculus
- Molecule
- Receptor-type tyrosine-protein phosphatase F; Liprin-alpha-3
- EC
- 3.1.3.48
- UniProt
- P10586, P60469
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.85 · 8 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase F (EC 3.1.3.48) | protein | 575 | 35% helix, 21% strand | P10586 |
| B | Receptor-type tyrosine-protein phosphatase F (EC 3.1.3.48) | protein | 571 | 35% helix, 22% strand | P10586 |
| C | Receptor-type tyrosine-protein phosphatase F (EC 3.1.3.48) | protein | 575 | 34% helix, 21% strand | P10586 |
| D | Receptor-type tyrosine-protein phosphatase F (EC 3.1.3.48) | protein | 568 | 35% helix, 21% strand | P10586 |
| E | Liprin-alpha-3 | protein | 266 | 67% helix, 0% strand | P60469 |
| F | Liprin-alpha-3 | protein | 264 | 69% helix, 0% strand | P60469 |
| H | Liprin-alpha-3 | protein | 231 | 69% helix, 0% strand | P60469 |
| G | Liprin-alpha-3 | protein | 15 | 33% helix, 0% strand | P60469 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D, E
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 2 copies · chains C, D
- P6G · Hexaethylene glycol · additive · chains D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.83 | 0.85 | 90 | empty |
| 2 | 818 | 0.82 | 0.85 | 72 | empty |
| 3 | 751 | 0.79 | 0.82 | 67 | empty |
| 4 | 411 | 0.78 | 0.87 | 40 | empty |
| 5 | 534 | 0.78 | 0.85 | 54 | empty |
Interfaces
11 interfaces between chains.
- D–H · 1190 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1138 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 1120 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1116 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1050 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6KR4 · Crystal structure of the liprin-ALPHA3_SAM123/LAR_D1D2 complex · the same entry in another collection · chain H against H, TM-score 1.00
- P10586 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase F… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P10586
- Every structure of UniProt P60469
- Elsewhere: RCSB PDB 6KR4 · PDBe 6KR4 · UniProt P10586 · UniProt P60469
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