SAXSdb — 4pbv

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

NT-3 growth factor receptor

Gallus gallus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Protein-tyrosine phosphatase CRYPalpha1 isoform × 1 （Q90815） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein-tyrosine phosphatase CRYPalpha1 isoform × 1 （Q90815） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTRK3_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–259； UniProt 32–302 Author chain B； PDBConstruct 4–259； UniProt 32–302

Protein-tyrosine phosphatase CRYPalpha1 isoform

Gallus gallus

UniProt Q90815

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	NT-3 growth factor receptor × 1 （Q91044） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	NT-3 growth factor receptor × 1 （Q91044） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q90815_CHICK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 4–291； UniProt 29–316 Author chain D； PDBConstruct 4–291； UniProt 29–316 Author chain E； PDBConstruct 4–291； UniProt 29–316

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	4pbv
Deposition date deposition_date	2014-04-14
Structure title title	Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC
Keywords keywords	Signaling protein, Synapse Cell signalling Cell surface receptor; 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.

4pbv__assembly_2__model_1

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

Download this curve (.dat)

4pbv__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pbv__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.25 Å
Rg (electron density)	24.03 Å
Total Rg	24.91 Å
Atom count	3537
Residues	449
Excluded volume	62485 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pbv__assembly_1__model_1`	Dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4pbv__assembly_2__model_1`	Dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4pbv__assembly_3__model_1`	Monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	NT-3 growth factor receptor
Molecular weight formula_weight	30399.4 kDa
EC 编号 ec_number	2.7.10.1
Mutation mutation	N163Q, N232Q, N259Q, N267Q and N294Q
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	8734

ETGCPANCLCSKTDINCKKPDDGNLFPLLEGQDSRNITSIHIENWKNLQTLNAVDMELYTGLQRLTIRNSGLRNIQPRAFAKNPHLRYIDLSGNRLTTLSWQLFQTLRLFDLRLERNPFQCSCDIRWIQLWQEKGEANLQSQQLHCMNLDTAVILLRNMNITQCDLPEISVSHVNLTVREGENAVITCQGSGSPLPDVDWTVADLHSINTHQTNLQWTNVHAIQLTLVNVTSEDNGFLLTCIAENVVGMSQASVLLTVYGTKHHHHHH

Source Source

Source organism organism	Gallus gallus
Common name common_name	Chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Protein-tyrosine phosphatase CRYPalpha1 isoform
Molecular weight formula_weight	32721.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

ETGESPPVFIKKPVDQIGVSGGVASFVCQATGDPKPRVTWNKKGKKVNSQRFETIEFDESAGAVLRIQPLRTPRDENIYECVAQNPHGEVTVHAKLTVLREDQLPPGFPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSTSNGRIKQLRSGGLQIESSEETDQGKYECVASNSAGVRYSSPANLYVRVRRVAPRFSILPVSHEIMPGGNVNITCVAVGSPMPYVKWMQGAEDLTPEDDMPVGRNVLELTDVKDSANYTCVAMSSLGVIEAVAQITVKSKGHHHHHH

Source Source

Source organism organism	Gallus gallus
Common name common_name	Chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	118

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4pbvc1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4pbvc2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4pbvd1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4pbvd2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4pbve1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4pbve2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	4pbvC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4pbvC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4pbvD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4pbvD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4pbvE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4pbvE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	68.300 Å
Unit-cell length b length_b	122.160 Å
Unit-cell length c length_c	98.610 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	92.790 Å
R factor r_factor	0.2105
R_work r_work	0.2086
R_free r_free	0.2470

Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC

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

NT-3 growth factor receptor

State in the Current Structure

Other States of the Same Protein in the Database

Protein-tyrosine phosphatase CRYPalpha1 isoform

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

4pbv__assembly_2__model_1

4pbv__assembly_2__model_1 | I(q)

4pbv__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC

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

NT-3 growth factor receptor

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-tyrosine phosphatase CRYPalpha1 isoform

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

4pbv__assembly_2__model_1

4pbv__assembly_2__model_1 | I(q)

4pbv__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)