5YBZ | pdb_00005ybz

High resolution structure of complement C1q-like protein 3 C1q domain

PDB DOI: https://doi.org/10.2210/pdb5YBZ/pdb

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

Deposited: 2017-09-05 Released: 2018-10-03
Deposition Author(s): Liu, H., Li, Z., Xu, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.186 (Depositor), 0.172 (DCC)
R-Value Work:
0.152 (Depositor)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5YBZ

This is version 1.1 of the entry. See complete history.

Literature

High resolution structure of complement C1q-like protein 3 C1q domain

Liu, H., Li, Z., Xu, F.

To be published.

Macromolecule Content

Total Structure Weight: 46.46 kDa
Atom Count: 3,584
Modeled Residue Count: 405
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C1q-like protein 3	A, B [auth C], C [auth D]	138	Mus musculus	Mutation(s): 0 Gene Names: C1ql3, C1ql, Ctrp13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ESN4 (Mus musculus) Explore Q9ESN4 Go to UniProtKB: Q9ESN4
IMPC: MGI:2387350
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ESN4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain H [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] K [auth C] L [auth C] F [auth A], G [auth A], H [auth A], K [auth C], L [auth C], M [auth C], Q [auth D], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Focus chain R [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth D] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain D [auth A]	D [auth A], E [auth A], P [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain P [auth D] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain P [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain J [auth A] MOL2 format, chain N [auth C] MOL2 format, chain J [auth A] mmCIF format, chain N [auth C] mmCIF format, chain J [auth A]	J [auth A], N [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.186 (Depositor), 0.172 (DCC)
R-Value Work: 0.152 (Depositor)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.027	α = 90
b = 79.213	β = 90
c = 87.495	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-10-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-10-03
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.