6ZBP | pdb_00006zbp

H11-H4 complex with SARS-CoV-2

PDB DOI: https://doi.org/10.2210/pdb6ZBP/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Lama glama
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2020-06-08 Released: 2020-07-29
Deposition Author(s): Naismith, J.H., Huo, J., Mikolajek, H., Ward, P., Dumoux, M., Owens, R.J., LeBas, A.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

H11-D4 complex with SARS-CoV-2 RBD

Naismith, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 39.08 kDa
Atom Count: 2,716
Modeled Residue Count: 323
Deposited Residue Count: 344
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth EEE]	210	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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth EEE]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H11-H4	B [auth FFF]	134	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth EEE] MOL2 format, chain C [auth EEE] mmCIF format, chain C [auth EEE]	C [auth EEE]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth EEE] Interactions & Density Focus chain C [auth EEE]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth FFF] MOL2 format, chain D [auth FFF] mmCIF format, chain D [auth FFF]	D [auth FFF]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth FFF] Interactions & Density Focus chain D [auth FFF]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.217 (Depositor), 0.220 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.15	α = 90
b = 73.15	β = 90
c = 131.67	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	100209/Z/12/Z

Revision History (Full details and data files)

Version 1.0: 2020-07-29
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary