6DLF | pdb_00006dlf

Crystal structure of NTRI homodimer

PDB DOI: https://doi.org/10.2210/pdb6DLF/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2018-06-01 Released: 2019-04-10
Deposition Author(s): Ranaivoson, F.M., Turk, L.S., Ozkan, E., Montelione, G.T., Comoletti, D.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free:
0.304 (Depositor), 0.304 (DCC)
R-Value Work:
0.274 (Depositor), 0.278 (DCC)
R-Value Observed:
0.275 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structure of a heterodimer of neuronal cell surface proteins

Ranaivoson, F.M., Turk, L.S., Ozkan, E., Montelione, G.T., Comoletti, D.

(2019) Structure

Macromolecule Content

Total Structure Weight: 68.85 kDa
Atom Count: 3,468
Modeled Residue Count: 470
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurotrimin	A, B	306	Homo sapiens	Mutation(s): 0 Gene Names: NTM, IGLON2, NT, UNQ297/PRO337
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P121 (Homo sapiens) Explore Q9P121 Go to UniProtKB: Q9P121
PHAROS: Q9P121 GTEx: ENSG00000182667
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9P121
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q9P121-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	D [auth A], E [auth A], F [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free: 0.304 (Depositor), 0.304 (DCC)
R-Value Work: 0.274 (Depositor), 0.278 (DCC)
R-Value Observed: 0.275 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.517	α = 90
b = 101.996	β = 90
c = 134.025	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1450895

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2019-11-27
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary