6U7G

HCoV-229E RBD Class V in complex with human APN

• PDB DOI: https://doi.org/10.2210/pdb6U7G/pdb

• Classification: HYDROLASE/VIRAL PROTEIN
• Organism(s): Homo sapiens, Human coronavirus 229E
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-09-02 Released: 2019-11-13 
• Deposition Author(s): Tomlinson, A., Li, Z., Rini, J.M.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.218 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 243.44 kDa 
• Atom Count: 17,357 
• Modelled Residue Count: 2,027 
• Deposited Residue Count: 2,102 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N	A, B	906	Homo sapiens	Mutation(s): 0  Gene Names: ANPEP, APN, CD13, PEPN EC: 3.4.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for P15144 (Homo sapiens) Explore P15144  Go to UniProtKB:  P15144
PHAROS:  P15144 GTEx:  ENSG00000166825

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein	C, D	145	Human coronavirus 229E	Mutation(s): 0
UniProt
Find proteins for Q1HVK2 (Human coronavirus 229E) Explore Q1HVK2  Go to UniProtKB:  Q1HVK2

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth C], U [auth C], V [auth D], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	I [auth A], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.218 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m36u7g

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.555	α = 90
b = 98.682	β = 104.6
c = 147.525	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Currently 6U7G does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): Tomlinson, A., Li, Z., Rini, J.M.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2020-05-06
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary