5O0O

Deglycosylated Nogo Receptor with native disulfide structure 5

PDB DOI: https://doi.org/10.2210/pdb5O0O/pdb

Classification: SIGNALING PROTEIN
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2017-05-16 Released: 2017-10-18
Deposition Author(s): Pronker, M.F., Janssen, B.J.C.
Funding Organization(s): NWO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.207
R-Value Work: 0.167
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 297.38 kDa
Atom Count: 21,913
Modelled Residue Count: 2,507
Deposited Residue Count: 2,584
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reticulon-4 receptor	A, B, C, D, E A, B, C, D, E, F, G, H	323	Mus musculus	Mutation(s): 0 Gene Names: Rtn4r, Ngr1, Nogor
UniProt
Find proteins for Q99PI8 (Mus musculus) Explore Q99PI8 Go to UniProtKB: Q99PI8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99PI8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AD [auth G] SDF format, chain BA [auth B] SDF format, chain BD [auth G] SDF format, chain CA [auth B] SDF format, chain CD [auth G] SDF format, chain I [auth A] SDF format, chain IB [auth D] SDF format, chain J [auth A] SDF format, chain JB [auth D] SDF format, chain JC [auth F] SDF format, chain K [auth A] SDF format, chain KB [auth D] SDF format, chain KC [auth F] SDF format, chain LC [auth F] SDF format, chain PD [auth H] SDF format, chain QD [auth H] SDF format, chain RA [auth C] SDF format, chain RD [auth H] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain VB [auth E] SDF format, chain WB [auth E] SDF format, chain XB [auth E] MOL2 format, chain AA [auth B] MOL2 format, chain AD [auth G] MOL2 format, chain BA [auth B] MOL2 format, chain BD [auth G] MOL2 format, chain CA [auth B] MOL2 format, chain CD [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain JC [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain KC [auth F] MOL2 format, chain LC [auth F] MOL2 format, chain PD [auth H] MOL2 format, chain QD [auth H] MOL2 format, chain RA [auth C] MOL2 format, chain RD [auth H] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain VB [auth E] MOL2 format, chain WB [auth E] MOL2 format, chain XB [auth E]	AA [auth B] AD [auth G] BA [auth B] BD [auth G] CA [auth B] AA [auth B], AD [auth G], BA [auth B], BD [auth G], CA [auth B], CD [auth G], I [auth A], IB [auth D], J [auth A], JB [auth D], JC [auth F], K [auth A], KB [auth D], KC [auth F], LC [auth F], PD [auth H], QD [auth H], RA [auth C], RD [auth H], SA [auth C], TA [auth C], VB [auth E], WB [auth E], XB [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain AD [auth G] Focus chain BA [auth B] Focus chain BD [auth G] Focus chain CA [auth B] Focus chain CD [auth G] Focus chain I [auth A] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain JC [auth F] Focus chain K [auth A] Focus chain KB [auth D] Focus chain KC [auth F] Focus chain LC [auth F] Focus chain PD [auth H] Focus chain QD [auth H] Focus chain RA [auth C] Focus chain RD [auth H] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain VB [auth E] Focus chain WB [auth E] Focus chain XB [auth E] Interactions & Density Focus chain AA [auth B] Focus chain AD [auth G] Focus chain BA [auth B] Focus chain BD [auth G] Focus chain CA [auth B] Focus chain CD [auth G] Focus chain I [auth A] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain JC [auth F] Focus chain K [auth A] Focus chain KB [auth D] Focus chain KC [auth F] Focus chain LC [auth F] Focus chain PD [auth H] Focus chain QD [auth H] Focus chain RA [auth C] Focus chain RD [auth H] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain VB [auth E] Focus chain WB [auth E] Focus chain XB [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain L [auth A] SDF format, chain LB [auth D] SDF format, chain M [auth A] SDF format, chain MC [auth F] SDF format, chain N [auth A] SDF format, chain SD [auth H] MOL2 format, chain DA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MC [auth F] MOL2 format, chain N [auth A] MOL2 format, chain SD [auth H]	DA [auth B] L [auth A] LB [auth D] M [auth A] MC [auth F] DA [auth B], L [auth A], LB [auth D], M [auth A], MC [auth F], N [auth A], SD [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain L [auth A] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MC [auth F] Focus chain N [auth A] Focus chain SD [auth H] Interactions & Density Focus chain DA [auth B] Focus chain L [auth A] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MC [auth F] Focus chain N [auth A] Focus chain SD [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain AC [auth E] SDF format, chain AE [auth H] SDF format, chain BB [auth C] SDF format, chain BC [auth E] SDF format, chain BE [auth H] SDF format, chain CB [auth C] SDF format, chain CC [auth E] SDF format, chain CE [auth H] SDF format, chain DB [auth C] SDF format, chain DC [auth E] SDF format, chain DD [auth G] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain EC [auth E] SDF format, chain ED [auth G] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain FC [auth E] SDF format, chain FD [auth G] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain GC [auth E] SDF format, chain GD [auth G] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain HC [auth E] SDF format, chain HD [auth G] SDF format, chain IA [auth B] SDF format, chain IC [auth E] SDF format, chain ID [auth G] SDF format, chain JA [auth B] SDF format, chain JD [auth G] SDF format, chain KA [auth B] SDF format, chain KD [auth G] SDF format, chain LA [auth B] SDF format, chain LD [auth G] SDF format, chain MA [auth B] SDF format, chain MB [auth D] SDF format, chain MD [auth G] SDF format, chain NA [auth B] SDF format, chain NB [auth D] SDF format, chain NC [auth F] SDF format, chain ND [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth D] SDF format, chain OC [auth F] SDF format, chain OD [auth G] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain PB [auth D] SDF format, chain PC [auth F] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth D] SDF format, chain QC [auth F] SDF format, chain R [auth A] SDF format, chain RB [auth D] SDF format, chain RC [auth F] SDF format, chain S [auth A] SDF format, chain SB [auth D] SDF format, chain SC [auth F] SDF format, chain T [auth A] SDF format, chain TB [auth D] SDF format, chain TC [auth F] SDF format, chain TD [auth H] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain UB [auth D] SDF format, chain UC [auth F] SDF format, chain UD [auth H] SDF format, chain V [auth A] SDF format, chain VA [auth C] SDF format, chain VC [auth F] SDF format, chain VD [auth H] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain WC [auth F] SDF format, chain WD [auth H] SDF format, chain X [auth A] SDF format, chain XA [auth C] SDF format, chain XC [auth F] SDF format, chain XD [auth H] SDF format, chain Y [auth A] SDF format, chain YA [auth C] SDF format, chain YB [auth E] SDF format, chain YC [auth F] SDF format, chain YD [auth H] SDF format, chain Z [auth A] SDF format, chain ZA [auth C] SDF format, chain ZB [auth E] SDF format, chain ZC [auth F] SDF format, chain ZD [auth H] MOL2 format, chain AB [auth C] MOL2 format, chain AC [auth E] MOL2 format, chain AE [auth H] MOL2 format, chain BB [auth C] MOL2 format, chain BC [auth E] MOL2 format, chain BE [auth H] MOL2 format, chain CB [auth C] MOL2 format, chain CC [auth E] MOL2 format, chain CE [auth H] MOL2 format, chain DB [auth C] MOL2 format, chain DC [auth E] MOL2 format, chain DD [auth G] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain EC [auth E] MOL2 format, chain ED [auth G] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain FC [auth E] MOL2 format, chain FD [auth G] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain GC [auth E] MOL2 format, chain GD [auth G] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain HC [auth E] MOL2 format, chain HD [auth G] MOL2 format, chain IA [auth B] MOL2 format, chain IC [auth E] MOL2 format, chain ID [auth G] MOL2 format, chain JA [auth B] MOL2 format, chain JD [auth G] MOL2 format, chain KA [auth B] MOL2 format, chain KD [auth G] MOL2 format, chain LA [auth B] MOL2 format, chain LD [auth G] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth D] MOL2 format, chain MD [auth G] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain NC [auth F] MOL2 format, chain ND [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain OC [auth F] MOL2 format, chain OD [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth D] MOL2 format, chain PC [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth D] MOL2 format, chain QC [auth F] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth D] MOL2 format, chain RC [auth F] MOL2 format, chain S [auth A] MOL2 format, chain SB [auth D] MOL2 format, chain SC [auth F] MOL2 format, chain T [auth A] MOL2 format, chain TB [auth D] MOL2 format, chain TC [auth F] MOL2 format, chain TD [auth H] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain UB [auth D] MOL2 format, chain UC [auth F] MOL2 format, chain UD [auth H] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain VC [auth F] MOL2 format, chain VD [auth H] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain WC [auth F] MOL2 format, chain WD [auth H] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain XC [auth F] MOL2 format, chain XD [auth H] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain YB [auth E] MOL2 format, chain YC [auth F] MOL2 format, chain YD [auth H] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth E] MOL2 format, chain ZC [auth F] MOL2 format, chain ZD [auth H]	AB [auth C] AC [auth E] AE [auth H] BB [auth C] BC [auth E] AB [auth C], AC [auth E], AE [auth H], BB [auth C], BC [auth E], BE [auth H], CB [auth C], CC [auth E], CE [auth H], DB [auth C], DC [auth E], DD [auth G], EA [auth B], EB [auth C], EC [auth E], ED [auth G], FA [auth B], FB [auth C], FC [auth E], FD [auth G], GA [auth B], GB [auth C], GC [auth E], GD [auth G], HA [auth B], HB [auth C], HC [auth E], HD [auth G], IA [auth B], IC [auth E], ID [auth G], JA [auth B], JD [auth G], KA [auth B], KD [auth G], LA [auth B], LD [auth G], MA [auth B], MB [auth D], MD [auth G], NA [auth B], NB [auth D], NC [auth F], ND [auth G], O [auth A], OA [auth B], OB [auth D], OC [auth F], OD [auth G], P [auth A], PA [auth B], PB [auth D], PC [auth F], Q [auth A], QA [auth B], QB [auth D], QC [auth F], R [auth A], RB [auth D], RC [auth F], S [auth A], SB [auth D], SC [auth F], T [auth A], TB [auth D], TC [auth F], TD [auth H], U [auth A], UA [auth C], UB [auth D], UC [auth F], UD [auth H], V [auth A], VA [auth C], VC [auth F], VD [auth H], W [auth A], WA [auth C], WC [auth F], WD [auth H], X [auth A], XA [auth C], XC [auth F], XD [auth H], Y [auth A], YA [auth C], YB [auth E], YC [auth F], YD [auth H], Z [auth A], ZA [auth C], ZB [auth E], ZC [auth F], ZD [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth C] Focus chain AC [auth E] Focus chain AE [auth H] Focus chain BB [auth C] Focus chain BC [auth E] Focus chain BE [auth H] Focus chain CB [auth C] Focus chain CC [auth E] Focus chain CE [auth H] Focus chain DB [auth C] Focus chain DC [auth E] Focus chain DD [auth G] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain EC [auth E] Focus chain ED [auth G] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain FC [auth E] Focus chain FD [auth G] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth E] Focus chain GD [auth G] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain HC [auth E] Focus chain HD [auth G] Focus chain IA [auth B] Focus chain IC [auth E] Focus chain ID [auth G] Focus chain JA [auth B] Focus chain JD [auth G] Focus chain KA [auth B] Focus chain KD [auth G] Focus chain LA [auth B] Focus chain LD [auth G] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain MD [auth G] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain NC [auth F] Focus chain ND [auth G] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain OC [auth F] Focus chain OD [auth G] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain PC [auth F] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain QC [auth F] Focus chain R [auth A] Focus chain RB [auth D] Focus chain RC [auth F] Focus chain S [auth A] Focus chain SB [auth D] Focus chain SC [auth F] Focus chain T [auth A] Focus chain TB [auth D] Focus chain TC [auth F] Focus chain TD [auth H] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth D] Focus chain UC [auth F] Focus chain UD [auth H] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VC [auth F] Focus chain VD [auth H] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WC [auth F] Focus chain WD [auth H] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XC [auth F] Focus chain XD [auth H] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain YC [auth F] Focus chain YD [auth H] Focus chain Z [auth A] Focus chain ZA [auth C] Focus chain ZB [auth E] Focus chain ZC [auth F] Focus chain ZD [auth H] Interactions & Density Focus chain AB [auth C] Focus chain AC [auth E] Focus chain AE [auth H] Focus chain BB [auth C] Focus chain BC [auth E] Focus chain BE [auth H] Focus chain CB [auth C] Focus chain CC [auth E] Focus chain CE [auth H] Focus chain DB [auth C] Focus chain DC [auth E] Focus chain DD [auth G] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain EC [auth E] Focus chain ED [auth G] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain FC [auth E] Focus chain FD [auth G] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth E] Focus chain GD [auth G] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain HC [auth E] Focus chain HD [auth G] Focus chain IA [auth B] Focus chain IC [auth E] Focus chain ID [auth G] Focus chain JA [auth B] Focus chain JD [auth G] Focus chain KA [auth B] Focus chain KD [auth G] Focus chain LA [auth B] Focus chain LD [auth G] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain MD [auth G] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain NC [auth F] Focus chain ND [auth G] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain OC [auth F] Focus chain OD [auth G] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain PC [auth F] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain QC [auth F] Focus chain R [auth A] Focus chain RB [auth D] Focus chain RC [auth F] Focus chain S [auth A] Focus chain SB [auth D] Focus chain SC [auth F] Focus chain T [auth A] Focus chain TB [auth D] Focus chain TC [auth F] Focus chain TD [auth H] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth D] Focus chain UC [auth F] Focus chain UD [auth H] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VC [auth F] Focus chain VD [auth H] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WC [auth F] Focus chain WD [auth H] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XC [auth F] Focus chain XD [auth H] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain YC [auth F] Focus chain YD [auth H] Focus chain Z [auth A] Focus chain ZA [auth C] Focus chain ZB [auth E] Focus chain ZC [auth F] Focus chain ZD [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.207
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.49	α = 90
b = 168.49	β = 90
c = 256.18	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-10-18

Deposition Author(s):

Pronker, M.F.

Janssen, B.J.C.

Funding Organization	Location	Grant Number
NWO	Netherlands	Vidi 723.012.002

Revision History (Full details and data files)

Version 1.0: 2017-10-18
Type: Initial release
Version 1.1: 2017-11-08
Changes: Database references
Version 1.2: 2017-11-15
Changes: Database references, Structure summary
Version 1.3: 2018-01-24
Changes: Source and taxonomy
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary