6Z2M
H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex
- PDB DOI: https://doi.org/10.2210/pdb6Z2M/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens, Lama glama
- Expression System: Homo sapiens, Escherichia coli
- Mutation(s): No 
- Deposited: 2020-05-17 Released: 2020-06-03 
- Funding Organization(s): Wellcome Trust, Engineering and Physical Sciences Research Council
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.71 Å
- R-Value Free: 0.241 
- R-Value Work: 0.198 
- R-Value Observed: 0.200 
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Spike glycoprotein | A, D [auth E] | 197 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0  Gene Names: S, 2 | |
UniProt | |||||
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0DTC2 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
CR3022 antibody | B, E [auth H] | 216 | Homo sapiens | 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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
CR3022 antibody | C, F [auth L] | 219 | Homo sapiens | 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: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
nanobody D4 | G [auth F], H [auth D] | 127 | Lama glama | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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 | I [auth A], J [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.71 Å
- R-Value Free: 0.241 
- R-Value Work: 0.198 
- R-Value Observed: 0.200 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 149.717 | α = 90 |
b = 150.395 | β = 90 |
c = 119.537 | γ = 90 |
Software Name | Purpose |
---|---|
XDS | data reduction |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-06-03  Deposition Author(s): Naismith, J.H., Ren, J., Zhou, D., Zhao, Y., Stuart, D.I.
Funding Organization | Location | Grant Number |
---|---|---|
Wellcome Trust | United Kingdom | 100209/Z/12/Z |
Engineering and Physical Sciences Research Council | United Kingdom | EP/S025243/1. |
Revision History (Full details and data files)
- Version 1.0: 2020-06-03
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary