1x27

Crystal Structure of Lck SH2-SH3 with SH2 binding site of p130Cas

Method: X-RAY DIFFRACTION

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

Proto-oncogene tyrosine-protein kinase LCK

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	CRK-associated substrate × 6 （Q63767） SODIUM ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LCK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–167； UniProt 63–225 Author chain B； PDBConstruct 5–167； UniProt 63–225 Author chain C； PDBConstruct 5–167； UniProt 63–225 Author chain D； PDBConstruct 5–167； UniProt 63–225 Author chain E； PDBConstruct 5–167； UniProt 63–225 Author chain F； PDBConstruct 5–167； UniProt 63–225

CRK-associated substrate

OrganismNot specified

UniProt Q63767

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Proto-oncogene tyrosine-protein kinase LCK × 6 （P06239） SODIUM ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCA1_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–9； UniProt 759–767 Author chain J； PDBConstruct 1–9； UniProt 759–767 Author chain K； PDBConstruct 1–9； UniProt 759–767 Author chain L； PDBConstruct 1–9； UniProt 759–767 Author chain M； PDBConstruct 1–9； UniProt 759–767 Author chain N； PDBConstruct 1–9； UniProt 759–767

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	1x27
Deposition date deposition_date	2005-04-20
Structure title title	Crystal Structure of Lck SH2-SH3 with SH2 binding site of p130Cas
Keywords keywords	Lck-Cas complex, LCK phospho-peptide complex, High affinity LCK-Cas complex, SIGNALING PROTEIN; SIGNALING 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.

1x27__assembly_1__model_1

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

Download this curve (.dat)

1x27__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1x27__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.86 Å
Rg (electron density)	29.51 Å
Total Rg	30.51 Å
Atom count	8198
Residues	1007
Excluded volume	143560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1x27__assembly_1__model_1`	dodecameric （12）	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	Proto-oncogene tyrosine-protein kinase LCK
Molecular weight formula_weight	18879.0 kDa
EC 编号 ec_number	2.7.1.112
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	8245

GSHMNLVIALHSYEPSHDGDLGFEKGEQLRILEQSGEWWKAQSLTTGQEGFIPFNFVAKANSLEPEPWFFKNLSRKDAERQLLAPGNTHGSFLIRESESTAGSFSLSVRDFDQNQGEVVKHYKIRNLDNGGFYISPRITFPGLHELVRHYTNASDGLCTRLSRPCQT

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	CRK-associated substrate
Molecular weight formula_weight	1265.3 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N

MEDYDYVHL

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	47

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6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d1x27a1
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	d1x27a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

Domain ID domain_id	d1x27b1
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	d1x27b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

Domain ID domain_id	d1x27b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1x27c1
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	d1x27c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

Domain ID domain_id	d1x27c3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1x27d1
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	d1x27d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

Domain ID domain_id	d1x27e1
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	d1x27e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

Domain ID domain_id	d1x27f1
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	d1x27f2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.1 — SH2 domain

CATH v4.4 (12 domains)

Domain ID domain_id	1x27A01
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	1x27A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	1x27B01
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	1x27B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	1x27C01
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	1x27C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	1x27D01
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	1x27D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	1x27E01
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	1x27E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	1x27F01
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	1x27F02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

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Unit-cell length a length_a	77.415 Å
Unit-cell length b length_b	107.289 Å
Unit-cell length c length_c	166.389 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	24

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2470
R_work r_work	0.2470
R_free r_free	0.3170

Crystal Structure of Lck SH2-SH3 with SH2 binding site of p130Cas

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

Proto-oncogene tyrosine-protein kinase LCK

State in the Current Structure

Other States of the Same Protein in the Database

CRK-associated substrate

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

1x27__assembly_1__model_1

1x27__assembly_1__model_1 | I(q)

1x27__assembly_1__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of Lck SH2-SH3 with SH2 binding site of p130Cas

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

Proto-oncogene tyrosine-protein kinase LCK

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CRK-associated substrate

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

1x27__assembly_1__model_1

1x27__assembly_1__model_1 | I(q)

1x27__assembly_1__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. Citations (1)