6JBU | pdb_00006jbu

High resolution crystal structure of human FLRT3 LRR domain in complex with mouse CIRL3 Olfactomedin like domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.234 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

High resolution crystal structure of human FLRT3 LRR domain in complex with mouse CIRL3 Olfactomedin like domain

Liu, H., Li, Z., Xu, F.

To be published.

Macromolecule Content 

  • Total Structure Weight: 72.21 kDa 
  • Atom Count: 5,137 
  • Modeled Residue Count: 585 
  • Deposited Residue Count: 623 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adhesion G protein-coupled receptor L3276Mus musculusMutation(s): 0 
Gene Names: Adgrl3, Kiaa0768, Lec3, Lphn3
UniProt & NIH Common Fund Data Resources
Find proteins for Q80TS3 (Mus musculus)
Explore Q80TS3 
Go to UniProtKB:  Q80TS3
IMPC:  MGI:2441950
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80TS3
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucine-rich repeat transmembrane protein FLRT3347Homo sapiensMutation(s): 0 
Gene Names: FLRT3, KIAA1469, UNQ856/PRO1865
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZU0 (Homo sapiens)
Explore Q9NZU0 
Go to UniProtKB:  Q9NZU0
PHAROS:  Q9NZU0
GTEx:  ENSG00000125848 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZU0
Glycosylation
Glycosylation Sites: 2
Go to GlyGen: Q9NZU0-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG


Download:Ideal Coordinates CCD File
L [auth B],
M [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4

Query on PO4


Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO


Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
J [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA

Query on NA


Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
K [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.234 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.135α = 90
b = 121.135β = 90
c = 83.413γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.3: 2024-11-20
    Changes: Structure summary