9IUD | pdb_00009iud

High resolution structure of Lectin-Like ox-LDL Receptor 1 with BI-0115 in space group P 21 21 21

PDB DOI: https://doi.org/10.2210/pdb9IUD/pdb

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

Deposited: 2024-07-20 Released: 2025-07-23
Deposition Author(s): Khan, M.A., Arulandu, A.
Funding Organization(s): Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.241 (Depositor), 0.245 (DCC)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

High resolution structure of Lectin-Like ox-LDL Receptor 1 with BI-0115 in space group P 21 21 21

khan, M.A., Arulandu, A.

To be published.

Macromolecule Content

Total Structure Weight: 127.33 kDa
Atom Count: 9,286
Modeled Residue Count: 1,056
Deposited Residue Count: 1,104
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidized low-density lipoprotein receptor 1	A, B, C, D, E A, B, C, D, E, F, G, H	138	Homo sapiens	Mutation(s): 0 Gene Names: OLR1, CLEC8A, LOX1
UniProt & NIH Common Fund Data Resources
Find proteins for P78380 (Homo sapiens) Explore P78380 Go to UniProtKB: P78380
PHAROS: P78380 GTEx: ENSG00000173391
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78380
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NJT (Subject of Investigation/LOI) Query on NJT Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain S [auth E] SDF format, chain U [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain S [auth E] MOL2 format, chain U [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain S [auth E] mmCIF format, chain U [auth H]	I [auth A], J [auth A], S [auth E], U [auth H]	9-chloranyl-5-propyl-11~{H}-pyrido[2,3-b][1,4]benzodiazepin-6-one C₁₅ H₁₄ Cl N₃ O QTCZUCSALXBZQR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth E] Focus chain U [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth E] Focus chain U [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain T [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F]	K [auth A] L [auth A] M [auth A] N [auth C] O [auth D] K [auth A], L [auth A], M [auth A], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], T [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain T [auth F] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain T [auth F]