Research workbench
Structure of a complex between domain V of beta2-glycoprotein I and the fourth ligand-binding module from LDLR determined with Haddock
Analyse Structure of a complex between domain V of beta2-glycoprotein I and the fourth… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2KRI
- Type
- protein
- Length
- 120 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- NOT
- Source
- Homo sapiens
- Molecule
- Beta-2-glycoprotein 1; Low-density lipoprotein receptor
- UniProt
- P02749, P01130
- Ligands
- CA
Structure
solution nmr · resolution NOT · 2 distinct chains · 11% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-2-glycoprotein 1 | protein | 82 | 5% helix, 35% strand | P02749 |
| B | Low-density lipoprotein receptor | protein | 38 | 24% helix, 16% strand | P01130 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 463 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2KRI · Structure of a complex between domain V of BETA2-glycoprotein I and the fourth… · the same entry in another collection · chain A against A, TM-score 1.00
- P02749 · AlphaFold monomer V2.0 prediction for beta-2-glycoprotein 1 (P02749) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P01130 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor (P01130) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 P02749
- Every structure of UniProt P01130
- Elsewhere: RCSB PDB 2KRI · PDBe 2KRI · UniProt P02749 · UniProt P01130
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