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MolNFT v1 · #42722 · protein

Structure of a complex between domain V of BETA2-glycoprotein I and the fourth ligand-binding module from ldlr determined with haddock

2KRI · Beta-2-glycoprotein 1: “Structure of a complex between domain V of BETA2-glycoprotein I and the fourth ligand-binding module from…”. Solution nmr, 1 ligand (CA). MolNFT v1 #42722 on GenesisL1: 3D structure, binding sites and pockets…

PDB
2KRI
Type
protein
Length
120 residues
Chains
2
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Beta-2-glycoprotein 1; Low-density lipoprotein receptor
UniProt
P02749, P01130
Ligands
CA

Structure

solution nmr · 2 distinct chains · 11% helix, 29% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ABeta-2-glycoprotein 1protein825% helix, 35% strandP02749
BLow-density lipoprotein receptorprotein3824% helix, 16% strandP01130

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

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