8V8Z

Lipoprotein(a) Kringle IV domain 8 - Lp(a) KIV8 in complex with LY3473329

PDB DOI: https://doi.org/10.2210/pdb8V8Z/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-06 Released: 2024-05-08
Deposition Author(s): Hendle, J., Weichert, K., Sauder, J.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.260
R-Value Work: 0.217
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Lipoprotein(a) Kringle IV domains 7 and 8 - Lp(a) KIV7 and KIV8 in complex with LY3353871, LY3441732 and LY3473329

Hendle, J., Weichert, K., Sauder, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 33.41 kDa
Atom Count: 2,136
Modelled Residue Count: 239
Deposited Residue Count: 282
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apolipoprotein(a)	A, B, C	94	Homo sapiens	Mutation(s): 0 Gene Names: LPA EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08519 (Homo sapiens) Explore P08519 Go to UniProtKB: P08519
PHAROS: P08519 GTEx: ENSG00000198670
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08519
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AAK (Subject of Investigation/LOI) Query on A1AAK Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B]	D [auth B]	muvalaplin C₄₂ H₅₄ N₄ O₆ BRLGERLDHZRETI-BGBFCPIGSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.260
R-Value Work: 0.217
R-Value Observed: 0.219
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.755	α = 90
b = 75.179	β = 90
c = 93.314	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-05-08
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.