SAXSdb — 6npw

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

Symplekin

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Ssu72 ortholog, LD40846p × 2 （Q9VWE4） Ser2/Ser5 phosphorylated peptide × 1 PHOSPHATE ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYMPK_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–339； UniProt 19–351 Author chain C； PDBConstruct 7–339； UniProt 19–351

Ssu72 ortholog, LD40846p

Drosophila melanogaster

UniProt Q9VWE4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Symplekin × 2 （Q8MSU4） Ser2/Ser5 phosphorylated peptide × 1 PHOSPHATE ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9VWE4_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–200； UniProt 1–195 Author chain D； PDBConstruct 6–200； UniProt 1–195

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	6npw
Deposition date deposition_date	2019-01-18
Structure title title	SSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide
Keywords keywords	phosphatase, CTD of RNA pol II, 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.

6npw__assembly_1__model_1

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

Download this curve (.dat)

6npw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6npw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.54 Å
Rg (electron density)	38.62 Å
Total Rg	38.82 Å
Atom count	8242
Residues	1040
Excluded volume	147240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6npw__assembly_1__model_1`	pentameric （5）	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	Symplekin
Molecular weight formula_weight	37495.3 kDa
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	8452

GPGSGMTDEKTATARAKVVDWCNELVIASPSTKCELLAKVQETVLGSCAELAEEFLESVLSLAHDSNMEVRKQVVAFVEQVCKVKVELLPHVINVVSMLLRDNSAQVIKRVIQACGSIYKNGLQYLCSLMEPGDSAEQAWNILSLIKAQILDMIDNENDGIRTNAIKFLEGVVVLQSFADEDSLKRDGDFSLADVPDHCTLFRREKLQEEGNNILDILLQFHGTTHISSVNLIACTSSLCTIAKMRPIFMGAVVEAFKQLNANLPPTLTDSQVSSVRKSLKMQLQTLLKNRGAFEFASTIRGMLVDLGSSTNEIQKLIPKMDKQEMARRQKRILENAAQ

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 K-12

Entity 2 Entity 2 polymer

Description description	Ssu72 ortholog, LD40846p
Molecular weight formula_weight	23130.3 kDa
EC 编号 ec_number	3.1.3.-,3.1.3.16,3.1.3.41
Mutation mutation	C13D, D144N
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPGSGMTDPSKLAVAVVDSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPGMAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHMLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVMHMESMESVDNRPVHVLNVDVVNNAEDALMGAFVITDMINMMAKSTDLDNDIDELIQEFEERRKRVILHSVLFY

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 K-12

Entity 3 Entity 3 polymer

Description description	Ser2/Ser5 phosphorylated peptide
Molecular weight formula_weight	2139.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

SPSYSPTSPSYSPTSPSYS

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	210

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6npwA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	6npwB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	6npwB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	550 —

Domain ID domain_id	6npwC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	6npwD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	6npwD02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	550 —

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Unit-cell length a length_a	127.702 Å
Unit-cell length b length_b	127.702 Å
Unit-cell length c length_c	105.979 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	8

Space group space_group	P 4
Space-group number int_tables_number	75
Crystal system crystal_system	—

Resolution resolution	2.486 Å
Low-resolution limit resolution_low	48.943 Å
R factor r_factor	0.1908
R_work r_work	0.1892
R_free r_free	0.2349

SSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide

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

Symplekin

State in the Current Structure

Other States of the Same Protein in the Database

Ssu72 ortholog, LD40846p

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

6npw__assembly_1__model_1

6npw__assembly_1__model_1 | I(q)

6npw__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 (5)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

SSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide

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

Symplekin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ssu72 ortholog, LD40846p

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

6npw__assembly_1__model_1

6npw__assembly_1__model_1 | I(q)

6npw__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 (5)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)