SAXSdb — 6hgc

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

Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Polycomb protein Asx × 1 （Q9V727）	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CALYP_DROME
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–264； UniProt 43–306 Author chain A； PDBConstruct 271–341； UniProt 334–404 Author chain B； PDBConstruct 1–264； UniProt 43–306 Author chain B； PDBConstruct 271–310； UniProt 334–373

Polycomb protein Asx

Drosophila melanogaster

UniProt Q9V727

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso × 1 （Q7K5N4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASX_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–110； UniProt 209–318

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	6hgc
Deposition date deposition_date	2018-08-23
Structure title title	Structure of Calypso in complex with DEUBAD of ASX
Keywords keywords	Deubiquitinase, Polycomb group proteins, transcription, gene repression, HYDROLASE; HYDROLASE
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.

6hgc__assembly_1__model_1

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

Download this curve (.dat)

6hgc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6hgc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.24 Å
Rg (electron density)	26.82 Å
Total Rg	27.53 Å
Atom count	3209
Residues	400
Excluded volume	57038 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6hgc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6hgc__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso
Molecular weight formula_weight	38469.7 kDa
EC 编号 ec_number	3.4.19.12,3.4.19.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5208

ADGWLELESDPGLFTLLLKDFGCHDVQVEEVYDLQKPIESPYGFIFLFRWIEERRARRKIVETTAEIFVKDEEAISSIFFAQQVVPNSCATHALLSVLLNCNENNLQLGDTLSRLKTHTKGMSPENKGLAIGNTPELACAHNSHAMPQARRRLERTGAGVSSCRFTGEAFHFVSFVPINGQLFELDGLKPYPMNHGGWEDSEDWTDKFRRVMAERLGIATGEQDIRFNLMAVVPDRRIAITHKLKMLRTNQAIVSGTLQKLLKAGSGSGSARDLQSLLKNLDTEIAINEQHLADENDRRHMFKVDASRRTHNYDKFICTFLSMLAHQGVLGELVSQHLLPS

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Polycomb protein Asx
Molecular weight formula_weight	12353.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

KIDLETPDSILASTNLRALLNKQTFSLLPPLYQYNLIQLLPSVDREASELEQPSSSASGGSPSEAIRLSASCLNNEFFARACLEWRERLSEGEFTPENQLKLKTEAEREK

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso
Molecular weight formula_weight	34984.7 kDa
EC 编号 ec_number	3.4.19.12,3.4.19.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ADGWLELESDPGLFTLLLKDFGCHDVQVEEVYDLQKPIESPYGFIFLFRWIEERRARRKIVETTAEIFVKDEEAISSIFFAQQVVPNSCATHALLSVLLNCNENNLQLGDTLSRLKTHTKGMSPENKGLAIGNTPELACAHNSHAMPQARRRLERTGAGVSSCRFTGEAFHFVSFVPINGQLFELDGLKPYPMNHGGWEDSEDWTDKFRRVMAERLGIATGEQDIRFNLMAVVPDRRIAITHKLKMLRTNQAIVSGTLQKLLKAGSGSGSARDLQSLLKNLDTEIAINEQHLADENDRRHMFKVDASRRT

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6hgcA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	532 — Ubiquitin C-terminal Hydrolase UCH-l3
Homologous superfamily homologous superfamily	10 — Peptidase C12, ubiquitin carboxyl-terminal hydrolase

Domain ID domain_id	6hgcB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	532 — Ubiquitin C-terminal Hydrolase UCH-l3
Homologous superfamily homologous superfamily	10 — Peptidase C12, ubiquitin carboxyl-terminal hydrolase

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Unit-cell length a length_a	119.505 Å
Unit-cell length b length_b	119.505 Å
Unit-cell length c length_c	408.900 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	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.020 Å
Low-resolution limit resolution_low	72.729 Å
R factor r_factor	0.2695
R_work r_work	0.2680
R_free r_free	0.2917

Structure of Calypso in complex with DEUBAD of ASX

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

Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso

State in the Current Structure

Other States of the Same Protein in the Database

Polycomb protein Asx

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

6hgc__assembly_1__model_1

6hgc__assembly_1__model_1 | I(q)

6hgc__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Calypso in complex with DEUBAD of ASX

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

Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polycomb protein Asx

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

6hgc__assembly_1__model_1

6hgc__assembly_1__model_1 | I(q)

6hgc__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)