SAXSdb — 6lxt

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike protein S2, Spike protein S2

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	TETRAETHYLENE GLYCOL × 2 ZINC ION × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_SARS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–79； UniProt 910–988 Author chain A； PDBConstruct 86–130； UniProt 1162–1206 Author chain B； PDBConstruct 1–79； UniProt 910–988 Author chain B； PDBConstruct 86–130； UniProt 1162–1206 Author chain C； PDBConstruct 1–79； UniProt 910–988 Author chain C； PDBConstruct 86–130； UniProt 1162–1206 Author chain D； PDBConstruct 1–79； UniProt 910–988 Author chain D； PDBConstruct 86–130； UniProt 1162–1206 Author chain E； PDBConstruct 1–79； UniProt 910–988 Author chain E； PDBConstruct 86–130； UniProt 1162–1206 Author chain F； PDBConstruct 1–79； UniProt 910–988 Author chain F； PDBConstruct 86–130； UniProt 1162–1206

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6lxt
Deposition date deposition_date	2020-02-11
Structure title title	Structure of post fusion core of 2019-nCoV S2 subunit
Keywords keywords	2019-nCoV, HR1 and HR2 domain, VIRUS, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6lxt__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6lxt__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6lxt__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	30.33 Å
Rg (electron density)	31.24 Å
Total Rg	31.17 Å
Atom count	2557
Residues	337
Excluded volume	45434 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6lxt__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6lxt__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Spike protein S2, Spike protein S2
Molecular weight formula_weight	13979.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	5237

GVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVESGGRGGPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYGG

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
Common name common_name	2019-nCoV
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6lxtA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	6lxtB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	6lxtC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	6lxtD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	6lxtE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	6lxtF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	300 —

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Unit-cell length a length_a	51.240 Å
Unit-cell length b length_b	57.580 Å
Unit-cell length c length_c	115.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	47.320 Å
R factor r_factor	—
R_work r_work	0.2593
R_free r_free	0.2896

Structure of post fusion core of 2019-nCoV S2 subunit

1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike protein S2, Spike protein S2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6lxt__assembly_2__model_1

6lxt__assembly_2__model_1 | I(q)

6lxt__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structure of post fusion core of 2019-nCoV S2 subunit

1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike protein S2, Spike protein S2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6lxt__assembly_2__model_1

6lxt__assembly_2__model_1 | I(q)

6lxt__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)