SAXSdb — 4d8d

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

Tyrosine-protein kinase Fyn

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Protein Nef × 1 （P03406） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein Nef × 1 （P03406） GLYCEROL × 1 water × 2	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 1–58； UniProt 84–141 Author chain C； PDBConstruct 1–58； UniProt 84–141

Protein Nef

Human immunodeficiency virus type 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 2	Tyrosine-protein kinase Fyn × 1 （P06241） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein kinase Fyn × 1 （P06241） GLYCEROL × 1 water × 2	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 3–149； UniProt 58–204 Author chain D； PDBConstruct 3–149； UniProt 58–204

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	4d8d
Deposition date deposition_date	2012-01-10
Structure title title	Crystal structure of HIV-1 NEF Fyn-SH3 R96W variant
Keywords keywords	signaling molecules, TRANSFERASE-PROTEIN BINDING complex; TRANSFERASE/PROTEIN BINDING
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.

4d8d__assembly_2__model_1

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

Download this curve (.dat)

4d8d__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4d8d__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.46 Å
Rg (electron density)	17.99 Å
Total Rg	19.03 Å
Atom count	1368
Residues	163
Excluded volume	24300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4d8d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4d8d__assembly_2__model_1`	dimeric （2）	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	Tyrosine-protein kinase Fyn
Molecular weight formula_weight	6652.2 kDa
EC 编号 ec_number	2.7.10.2
Mutation mutation	R96W
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	2774

VTLFVALYDYEAWTEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPV

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

Entity 2 Entity 2 polymer

Description description	Protein Nef
Molecular weight formula_weight	17568.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKNC

Source Source

Source organism organism	Human immunodeficiency virus type 1
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11686
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4d8da_
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	d4d8db_
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	d4d8dc_
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	d4d8dd_
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	4d8dA00
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	4d8dB00
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	4d8dC00
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	4d8dD00
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	108.010 Å
Unit-cell length b length_b	108.010 Å
Unit-cell length c length_c	224.961 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	2.520 Å
Low-resolution limit resolution_low	52.513 Å
R factor r_factor	0.2135
R_work r_work	0.2121
R_free r_free	0.2376

Crystal structure of HIV-1 NEF Fyn-SH3 R96W variant

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

Tyrosine-protein kinase Fyn

State in the Current Structure

Other States of the Same Protein in the Database

Protein Nef

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

4d8d__assembly_2__model_1

4d8d__assembly_2__model_1 | I(q)

4d8d__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 (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)

Crystal structure of HIV-1 NEF Fyn-SH3 R96W variant

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

Tyrosine-protein kinase Fyn

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein Nef

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

4d8d__assembly_2__model_1

4d8d__assembly_2__model_1 | I(q)

4d8d__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 (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)