4CAJ

Crystallographic structure of the mouse SIGN-R1 CRD domain in complex with sialic acid

PDB DOI: https://doi.org/10.2210/pdb4CAJ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2013-10-08 Released: 2014-10-15
Deposition Author(s): Silva-Martin, N., Bartual, S.G., Hermoso, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.281
R-Value Work: 0.205
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 75.93 kDa
Atom Count: 4,976
Modelled Residue Count: 528
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD209 ANTIGEN-LIKE PROTEIN B	A, B, C, D	158	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q8CJ91 (Mus musculus) Explore Q8CJ91 Go to UniProtKB: Q8CJ91
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8CJ91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain I [auth A] SDF format, chain U [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain U [auth B]	EA [auth C], I [auth A], U [auth B]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain EA [auth C] Focus chain I [auth A] Focus chain U [auth B] Interactions & Density Focus chain EA [auth C] Focus chain I [auth A] Focus chain U [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain Y [auth B] SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth B] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] F [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], F [auth A], G [auth A], GA [auth C], H [auth A], HA [auth C], IA [auth C], JA [auth C], K [auth A], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth B], PA [auth D], QA [auth D], R [auth B], S [auth B], T [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain KA [auth D] SDF format, chain Q [auth B] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth C]	E [auth A], KA [auth D], Q [auth B], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain KA [auth D] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain KA [auth D] Focus chain Q [auth B] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain J [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain J [auth A]	FA [auth C], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth C] Focus chain J [auth A] Interactions & Density Focus chain FA [auth C] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.281
R-Value Work: 0.205
R-Value Observed: 0.209
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.2	α = 90
b = 94.47	β = 121.42
c = 76.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-10-15

Deposition Author(s):

Silva-Martin, N.

Bartual, S.G.

Hermoso, J.A.

Revision History (Full details and data files)

Version 1.0: 2014-10-15
Type: Initial release
Version 1.1: 2014-11-12
Changes: Database references
Version 1.2: 2015-07-22
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary