7C00

Crystal structure of the SRCR domain of human SCARA5.

• PDB DOI: https://doi.org/10.2210/pdb7C00/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-04-29 Released: 2020-09-16 
• Deposition Author(s): Yu, B., He, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.175 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 13.46 kDa 
• Atom Count: 999 
• Modelled Residue Count: 108 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scavenger receptor class A member 5	A	114	Homo sapiens	Mutation(s): 0  Gene Names: SCARA5, UNQ2938/PRO28700
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZMJ2 (Homo sapiens) Explore Q6ZMJ2  Go to UniProtKB:  Q6ZMJ2
PHAROS:  Q6ZMJ2 GTEx:  ENSG00000168079

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.175 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.167	α = 90
b = 48.802	β = 90
c = 70.771	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Yu, B., He, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	No. 91957102

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Refinement description