7DK2 | pdb_00007dk2

Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab

PDB DOI: https://doi.org/10.2210/pdb7DK2/pdb

Classification: IMMUNE SYSTEM/VIRAL PROTEIN
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2020-11-22 Released: 2021-12-08
Deposition Author(s): Wang, J., Jiao, S., Wang, R., Zhang, J., Zhang, M., Wang, M., Chen, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.304 (Depositor), 0.309 (DCC)
R-Value Work:
0.258 (Depositor), 0.267 (DCC)
R-Value Observed:
0.260 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7DK2

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Architectural versatility of spike neutralization by a SARS-CoV-2 antibody

Sun, Y., Liu, F.J., Guo, H.T., Wang, J., Wang, R., Zhang, M., Wang, M., Chen, S.

To be published.

Macromolecule Content

Total Structure Weight: 290.03 kDa
Atom Count: 19,459
Modeled Residue Count: 2,503
Deposited Residue Count: 2,640
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MW07 heavy chain	A, D, G, J	223	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MW07 light chain	B, E, H, K	214	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C, F, I, L	223	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C Focus chain F Focus chain I Focus chain L	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth L] SDF format, chain O [auth I] SDF format, chain N [auth F] SDF format, chain M [auth C] MOL2 format, chain P [auth L] MOL2 format, chain O [auth I] MOL2 format, chain N [auth F] MOL2 format, chain M [auth C] mmCIF format, chain P [auth L] mmCIF format, chain O [auth I] mmCIF format, chain N [auth F] mmCIF format, chain M [auth C]	M [auth C], N [auth F], O [auth I], P [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth C] Focus chain N [auth F] Focus chain O [auth I] Focus chain P [auth L] Interactions & Density Focus chain M [auth C] Focus chain N [auth F] Focus chain O [auth I] Focus chain P [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.304 (Depositor), 0.309 (DCC)
R-Value Work: 0.258 (Depositor), 0.267 (DCC)
R-Value Observed: 0.260 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.73	α = 90
b = 102.81	β = 107.16
c = 163.42	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-12-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-12-08
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.