4ZPT
Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 1)
- PDB DOI: https://doi.org/10.2210/pdb4ZPT/pdb
- Classification: Viral protein/Immune system
- Organism(s): Mus musculus, Betacoronavirus England 1
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2015-05-08 Released: 2015-10-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.59 Å
- R-Value Free: 0.244
- R-Value Work: 0.204
- R-Value Observed: 0.206
This is version 1.1 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 |
| D12 Fab Heavy chain | A, D [auth H] | 216 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| D12 Fab Light chain | B, F [auth L] | 214 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Spike glycoprotein | C [auth R], E [auth S] | 208 | Betacoronavirus England 1 | Mutation(s): 0 Gene Names: S, 3 |  |
UniProt | |||||
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N5Q8 Go to UniProtKB: K9N5Q8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | K9N5Q8 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | G [auth R], H [auth S] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.59 Å
- R-Value Free: 0.244
- R-Value Work: 0.204
- R-Value Observed: 0.206
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 74.452 | α = 90 |
| b = 128.79 | β = 90 |
| c = 170.871 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2015-10-21 Deposition Author(s): Joyce, M.G., Mascola, J.R., Graham, B.S., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2015-10-21
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
