3KBH

Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor

PDB DOI: https://doi.org/10.2210/pdb3KBH/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, Human coronavirus NL63
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2009-10-20 Released: 2009-12-15
Deposition Author(s): Wu, K., Li, W., Peng, G., Li, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free: 0.300
R-Value Work: 0.268
R-Value Observed: 0.270

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 340.26 kDa
Atom Count: 23,024
Modelled Residue Count: 2,812
Deposited Residue Count: 2,932
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A, C [auth B], E [auth C], G [auth D]	597	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, spike protein, UNQ868/PRO1885 EC: 3.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYF1
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B [auth E], D [auth F], F [auth G], H	136	Human coronavirus NL63	Mutation(s): 0 Gene Names: 2, human angiotensin-converting enzyme 2, S
UniProt
Find proteins for Q6Q1S2 (Human coronavirus NL63) Explore Q6Q1S2 Go to UniProtKB: Q6Q1S2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6Q1S2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth E] SDF format, chain L [auth E] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth F] SDF format, chain P [auth F] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth G] SDF format, chain T [auth G] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth H] SDF format, chain X [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth E] MOL2 format, chain L [auth E] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H]	I [auth A] J [auth A] K [auth E] L [auth E] M [auth B] I [auth A], J [auth A], K [auth E], L [auth E], M [auth B], N [auth B], O [auth F], P [auth F], Q [auth C], R [auth C], S [auth G], T [auth G], U [auth D], V [auth D], W [auth H], X [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth H] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free: 0.300
R-Value Work: 0.268
R-Value Observed: 0.270
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.764	α = 90
b = 77.764	β = 90
c = 631.095	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-12-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2018-04-18
Changes: Data collection
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary

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Help and Resources

3KBH

Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt