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 
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 
This is version 1.3 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(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 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(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 AnnotationsExpand | |||||
|
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | I [auth A] J [auth A] K [auth E] L [auth E] M [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
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 Name | Purpose |
---|---|
HKL-3000 | data collection |
AMoRE | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
Entry History 
Deposition Data
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