SAXSdb — 7czf

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

Ephrin type-A receptor 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 3	Envelope glycoprotein H × 1 （Q98142） Envelope glycoprotein L × 1 （Q76RG7） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 3	Envelope glycoprotein H × 1 （Q98142） Envelope glycoprotein L × 1 （Q76RG7） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EPHA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–179； UniProt 28–206 Author chain D； PDBConstruct 1–179； UniProt 28–206

Envelope glycoprotein H

Human herpesvirus 8

UniProt Q98142

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 3	Ephrin type-A receptor 2 × 1 （P29317） Envelope glycoprotein L × 1 （Q76RG7） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 3	Ephrin type-A receptor 2 × 1 （P29317） Envelope glycoprotein L × 1 （Q76RG7） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q98142_HHV8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–677； UniProt 22–698 Author chain E； PDBConstruct 1–677； UniProt 22–698

Envelope glycoprotein L

Human herpesvirus 8

UniProt Q76RG7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 3	Ephrin type-A receptor 2 × 1 （P29317） Envelope glycoprotein H × 1 （Q98142） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 3	Ephrin type-A receptor 2 × 1 （P29317） Envelope glycoprotein H × 1 （Q98142） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q76RG7_HHV8
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 5–151； UniProt 21–167 Author chain F； PDBConstruct 5–151； UniProt 21–167

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	7czf
Deposition date deposition_date	2020-09-08
Structure title title	Crystal structure of Kaposi Sarcoma associated herpesvirus (KSHV ) gHgL in complex with the ligand binding domian (LBD) of EphA2
Keywords keywords	glycoprotein, receptor, complex, virus entry, 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.

7czf__assembly_2__model_1

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

Download this curve (.dat)

7czf__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7czf__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	41.67 Å
Rg (electron density)	42.39 Å
Total Rg	42.18 Å
Atom count	7412
Residues	915
Excluded volume	132580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7czf__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7czf__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 (7)

Entity 1 Entity 1 polymer

Description description	Ephrin type-A receptor 2
Molecular weight formula_weight	21323.1 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	14901

EVVLLDFAAAGGELGWLTHPYGKGWDLMQNIMNDMPIYMYSVCNVMSGDQDNWLRTNWVYRGEAERIFIELKFTVRDCNSFPGGASSCKETFNLYYAESDLDYGTNFQKRLFTKIDTIAPDEITVSSDFEARHVKLNVEERSVGPLTRKGFYLAFQDIGACVALLSVRVYYKKCPELLQHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	75374.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

ATGALPTTATTITRSATQLINGRTNLSIELEFNGTSFFLNWQNLLNVITEPALTELWTSAEVAEDLRVTLKKRQSLFFPNKTVVISGDGHRYTCEVPTSSQTYNITKGFNYSALPGHLGGFGINARLVLGDIFASKWSLFARDTPEYRVFYPMNVMAVKFSISIGNNESGVALYGVVSEDFVVVTLHNRSKEANETASHLLFGLPDSLPSLKGHATYDELTFARNAKYALVAILPKDSYQTLLTENYTRIFLNMTESTPLEFTRTIQTRIVSIEARRACAAQEAAPDIFLVLFQMLVAHFLVARGIAEHRFVEVDCVCRQYAELYFLRRISRLCMPTFTTVGYNHTTLGAVAATQIARVSATKLASLPRSSQETVLAMVQLGARDGAVPSSILEGIAMVVEHMYTAYTYVYTLGDTERKLMLDIHTVLTDSCPPKDSGVSEKLLRTYLMFTSMCTNIELGEMIARFSKPDSLNIYRAFSPCFLGLRYDLHPAKLRAEAPQSSALTRTAVARGTSGFAELLHALHLDSLNLIPAINCSKITADKIIATVPLPHVTYIISSEALSNAVVYEVSEIFLKSAMFISAIKPDCSGFNFSQIDRHIPIVYNISTPRRGCPLCDSVIMSYDESDGLQSLMYVTNERVQTNLFLDKSPFFDNNNLHIHYLWLRDNGTVVEIRGMY

Source Source

Source organism organism	Human herpesvirus 8
Common name common_name	HHV-8
NCBI taxonomy ID ncbi_taxonomy_id	37296
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Envelope glycoprotein L
Molecular weight formula_weight	17088.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

DGIQYVALPCCAIQASAASTLPLFFAVHSIHFADPNHCNGVCIAKLRSKTGDITVETCVNGFNLRSFLVAVVRRLGSWASQENLRLLWYLQRSLTAYTVGFNATTADSSIHNVNIIIISVGKAMNRTGSVSGSQTRAKSSSRRAHAGQKGKHHHHHH

Source Source

Source organism organism	Human herpesvirus 8
Common name common_name	HHV-8
NCBI taxonomy ID ncbi_taxonomy_id	37296
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1041.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7czfB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3190 — Herpesvirus glycoprotein H, C-terminal domain

Domain ID domain_id	7czfE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3190 — Herpesvirus glycoprotein H, C-terminal domain

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Unit-cell length a length_a	80.803 Å
Unit-cell length b length_b	153.196 Å
Unit-cell length c length_c	275.228 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	31.650 Å
R factor r_factor	0.2409
R_work r_work	0.2393
R_free r_free	0.2721

Crystal structure of Kaposi Sarcoma associated herpesvirus (KSHV ) gHgL in complex with the ligand binding domian (LBD) of EphA2

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

Ephrin type-A receptor 2

State in the Current Structure

Other States of the Same Protein in the Database

Envelope glycoprotein H

State in the Current Structure

Other States of the Same Protein in the Database

Envelope glycoprotein L

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

7czf__assembly_2__model_1

7czf__assembly_2__model_1 | I(q)

7czf__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Kaposi Sarcoma associated herpesvirus (KSHV ) gHgL in complex with the ligand binding domian (LBD) of EphA2

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

Ephrin type-A receptor 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Envelope glycoprotein H

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Envelope glycoprotein L

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

7czf__assembly_2__model_1

7czf__assembly_2__model_1 | I(q)

7czf__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)