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), 0.190 (DCC)
R-Value Work:
0.152 (Depositor), 0.150 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	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 D [auth A] SDF format, chain E [auth A] SDF format, chain P [auth D] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain P [auth D] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain P [auth D]	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 J [auth A] SDF format, chain N [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth C]	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]