SAXSdb — 1efn

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

FYN TYROSINE KINASE

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	HIV-1 NEF PROTEIN × 2 （P03406） TRIMETHYL LEAD ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FYN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–59； UniProt 85–142 Author chain C； PDBConstruct 2–59； UniProt 85–142

HIV-1 NEF PROTEIN

Human immunodeficiency virus 1

UniProt P03406

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	FYN TYROSINE KINASE × 2 （P06241） TRIMETHYL LEAD ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEF_HV1BR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–152； UniProt 54–205 Author chain D； PDBConstruct 1–152； UniProt 54–205

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	1efn
Deposition date deposition_date	1996-06-29
Structure title title	HIV-1 NEF PROTEIN IN COMPLEX WITH R96I MUTANT FYN SH3 DOMAIN
Keywords keywords	;COMPLEX (SH3 DOMAIN-VIRAL ENHANCER), PROTO-ONCOGENE, TRANSFERASE, TYROSINE-PROTEIN KINASE, PHOSPHORYLATION, AIDS, MYRISTYLATION, GTP-BINDING, ATP-BINDING, SH3 DOMAIN, SH2 DOMAIN, PPII HELIX, PXXP MOTIF, COMPLEX (SH3 DOMAIN-VIRAL ENHANCER) complex ;; COMPLEX (SH3 DOMAIN/VIRAL ENHANCER)
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.

1efn__assembly_1__model_1

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

Download this curve (.dat)

1efn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1efn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.34 Å
Rg (electron density)	22.48 Å
Total Rg	23.42 Å
Atom count	2643
Residues	322
Excluded volume	46780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1efn__assembly_1__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	FYN TYROSINE KINASE
Molecular weight formula_weight	6652.2 kDa
EC 编号 ec_number	2.7.1.112
Mutation mutation	R96I
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2742

ALFVALYDYEAITEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVDS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	HIV-1 NEF PROTEIN
Molecular weight formula_weight	17809.0 kDa
Mutation mutation	T71R
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ACAWLEAQEEEEVGFPVRPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKN

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	TRIMETHYL LEAD ION
Molecular weight formula_weight	252.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1efna_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d1efnb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.102 — Regulatory factor Nef
Superfamily Superfamily superfamily	d.102.1 — Regulatory factor Nef
Family Family family	d.102.1.1 — Regulatory factor Nef

Domain ID domain_id	d1efnc_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d1efnd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.102 — Regulatory factor Nef
Superfamily Superfamily superfamily	d.102.1 — Regulatory factor Nef
Family Family family	d.102.1.1 — Regulatory factor Nef

CATH v4.4 (4 domains)

Domain ID domain_id	1efnA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	1efnB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	62 — Nef Regulatory Factor
Homologous superfamily homologous superfamily	10 — Nef Regulatory Factor

Domain ID domain_id	1efnC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	1efnD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	62 — Nef Regulatory Factor
Homologous superfamily homologous superfamily	10 — Nef Regulatory Factor

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Unit-cell length a length_a	107.800 Å
Unit-cell length b length_b	107.800 Å
Unit-cell length c length_c	229.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2820

HIV-1 NEF PROTEIN IN COMPLEX WITH R96I MUTANT FYN SH3 DOMAIN

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

FYN TYROSINE KINASE

State in the Current Structure

Other States of the Same Protein in the Database

HIV-1 NEF PROTEIN

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

1efn__assembly_1__model_1

1efn__assembly_1__model_1 | I(q)

1efn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)

HIV-1 NEF PROTEIN IN COMPLEX WITH R96I MUTANT FYN SH3 DOMAIN

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

FYN TYROSINE KINASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HIV-1 NEF PROTEIN

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

1efn__assembly_1__model_1

1efn__assembly_1__model_1 | I(q)

1efn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)