SAXSdb — 2vzd

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

ALPHA-PARVIN

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	PAXILLIN × 1 （P49023） TRIETHYLENE GLYCOL × 2 TETRAETHYLENE GLYCOL × 1 GLYCEROL × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PAXILLIN × 1 （P49023） TETRAETHYLENE GLYCOL × 1 GLYCEROL × 1 1,2-ETHANEDIOL × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PARVA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 242–372 Author chain B； PDBConstruct 1–131； UniProt 242–372

PAXILLIN

OrganismNot specified

UniProt P49023

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	ALPHA-PARVIN × 1 （Q9NVD7） TRIETHYLENE GLYCOL × 2 TETRAETHYLENE GLYCOL × 1 GLYCEROL × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	ALPHA-PARVIN × 1 （Q9NVD7） TETRAETHYLENE GLYCOL × 1 GLYCEROL × 1 1,2-ETHANEDIOL × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAXI_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–20； UniProt 1–20 Author chain D； PDBConstruct 1–20； UniProt 1–20

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	2vzd
Deposition date deposition_date	2008-07-31
Structure title title	Crystal structure of the C-terminal calponin homology domain of alpha parvin in complex with paxillin LD1 motif
Keywords keywords	;CALPONIN HOMOLOGY DOMAIN, CELL MEMBRANE, CELL ADHESION, METAL-BINDING, CYTOSKELETON, CELL JUNCTION, ACTIN-BINDING, PHOSPHOPROTEIN, MEMBRANE, LD1 MOTIF, LIM DOMAIN ;; CELL ADHESION
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.

2vzd__assembly_2__model_1

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

Download this curve (.dat)

2vzd__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vzd__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	16.39 Å
Rg (electron density)	14.92 Å
Total Rg	16.13 Å
Atom count	1173
Residues	140
Excluded volume	21249 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vzd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vzd__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 (7)

Entity 1 Entity 1 polymer

Description description	ALPHA-PARVIN
Molecular weight formula_weight	15155.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2942

SGRHERDAFDTLFDHAPDKLNVVKKTLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEGYFVPLHSFFLTPDSFEQKVLNVSFAFELMQDGGLEKPKPRPEDIVNCDLKSTLRVLYNLFTKYRNVE

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	PAXILLIN
Molecular weight formula_weight	2177.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

MDDLDALLADLESTTSHISK

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	85

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2vzdA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	10 — Calponin-like domain

Domain ID domain_id	2vzdB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	10 — Calponin-like domain

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Unit-cell length a length_a	133.123 Å
Unit-cell length b length_b	37.503 Å
Unit-cell length c length_c	70.244 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	28.640 Å
R factor r_factor	0.2190
R_work r_work	0.2170
R_free r_free	0.2550

Crystal structure of the C-terminal calponin homology domain of alpha parvin in complex with paxillin LD1 motif

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

ALPHA-PARVIN

State in the Current Structure

Other States of the Same Protein in the Database

PAXILLIN

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

2vzd__assembly_2__model_1

2vzd__assembly_2__model_1 | I(q)

2vzd__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the C-terminal calponin homology domain of alpha parvin in complex with paxillin LD1 motif

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

ALPHA-PARVIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PAXILLIN

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

2vzd__assembly_2__model_1

2vzd__assembly_2__model_1 | I(q)

2vzd__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)