5Z8X

Crystal structure of human LRRTM2

PDB DOI: https://doi.org/10.2210/pdb5Z8X/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2018-02-01 Released: 2018-10-10
Deposition Author(s): Yamagata, A., Fukai, S.
Funding Organization(s): JSPS/MEXT, JST

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.231
R-Value Work: 0.203
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 161.21 kDa
Atom Count: 10,756
Modelled Residue Count: 1,312
Deposited Residue Count: 1,384
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat transmembrane neuronal protein 2	A, B, C, D	346	Homo sapiens	Mutation(s): 1 Gene Names: LRRTM2, KIAA0416, LRRN2
UniProt & NIH Common Fund Data Resources
Find proteins for O43300 (Homo sapiens) Explore O43300 Go to UniProtKB: O43300
PHAROS: O43300 GTEx: ENSG00000146006
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43300
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth C] E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.231
R-Value Work: 0.203
R-Value Observed: 0.204
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.691	α = 90
b = 240.959	β = 90
c = 259.434	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-10

Deposition Author(s):

Yamagata, A.

Fukai, S.

Funding Organization	Location	Grant Number
JSPS/MEXT	Japan	JP16H04749
JST	Japan	JPMJCR12M5

Revision History (Full details and data files)

Version 1.0: 2018-10-10
Type: Initial release
Version 1.1: 2018-10-31
Changes: Data collection, Structure summary
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

5Z8X

Crystal structure of human LRRTM2

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)