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2qkm

The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SPBC3B9.21 protein

Schizosaccharomyces pombe

UniProt Q9P805

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 SPAC19A8.12 protein × 1 （O13828） ADENOSINE-5'-TRIPHOSPHATE × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 SPAC19A8.12 protein × 1 （O13828） ADENOSINE-5'-TRIPHOSPHATE × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 SPAC19A8.12 protein × 1 （O13828） water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 SPAC19A8.12 protein × 1 （O13828） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2qkl 2qkm 2qkm 2qkm 2qkm 5j3q 5j3q 5j3t 5j3y 5j3y 5jp4 5kq1

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q9P805_SCHPO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–127； UniProt 1–127 Author chain C； PDBConstruct 1–127； UniProt 1–127 Author chain E； PDBConstruct 1–127； UniProt 1–127 Author chain G； PDBConstruct 1–127； UniProt 1–127

SPAC19A8.12 protein

Schizosaccharomyces pombe

UniProt O13828

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 SPBC3B9.21 protein × 1 （Q9P805） ADENOSINE-5'-TRIPHOSPHATE × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 SPBC3B9.21 protein × 1 （Q9P805） ADENOSINE-5'-TRIPHOSPHATE × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 SPBC3B9.21 protein × 1 （Q9P805） water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 SPBC3B9.21 protein × 1 （Q9P805） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2a6t 2a6t

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2qkl 2qkm 2qkm 2qkm 2qkm 4a54 5j3t 5j3y 5j3y 5kq1 5kq4 5n2v

13 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name O13828_SCHPO
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–266； UniProt 1–266 Author chain D； PDBConstruct 1–266； UniProt 1–266 Author chain F； PDBConstruct 1–266； UniProt 1–266 Author chain H； PDBConstruct 1–266； UniProt 1–266

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_id2qkm
Deposition date deposition_date2007-07-11
Structure title titleThe crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex
Keywords keywordsProtein-Protein complex, Hydrolase; HYDROLASE
Experimental Method methodX-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.

2qkm__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2qkm__assembly_4__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2qkm__assembly_4__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）29.62 Å
Rg (electron density)29.77 Å
Total Rg30.37 Å
Atom count2622
Residues317
Excluded volume46817 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2qkm__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2qkm__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2qkm__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 2qkm__assembly_4__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 (4)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2qkmd1
Class classa — All alpha proteins
Fold Fold folda.242 — Dcp2 domain-like
Superfamily Superfamily superfamilya.242.1 — Dcp2 domain-like
Family Family familya.242.1.1 — Dcp2 box A domain
Domain ID domain_idd2qkmd2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.113 — Nudix
Superfamily Superfamily superfamilyd.113.1 — Nudix
Family Family familyd.113.1.7 — mRNA decapping enzyme-like
Domain ID domain_idd2qkmh1
Class classa — All alpha proteins
Fold Fold folda.242 — Dcp2 domain-like
Superfamily Superfamily superfamilya.242.1 — Dcp2 domain-like
Family Family familya.242.1.1 — Dcp2 box A domain
Domain ID domain_idd2qkmh2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.113 — Nudix
Superfamily Superfamily superfamilyd.113.1 — Nudix
Family Family familyd.113.1.7 — mRNA decapping enzyme-like

CATH v4.4 (12 domains)

Domain ID domain_id2qkmA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id2qkmB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1050 — Dcp2, box A domain
Domain ID domain_id2qkmB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily10 — Nucleoside Triphosphate Pyrophosphohydrolase
Domain ID domain_id2qkmC00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id2qkmD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1050 — Dcp2, box A domain
Domain ID domain_id2qkmD02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily10 — Nucleoside Triphosphate Pyrophosphohydrolase
Domain ID domain_id2qkmE00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id2qkmF01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1050 — Dcp2, box A domain
Domain ID domain_id2qkmF02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily10 — Nucleoside Triphosphate Pyrophosphohydrolase
Domain ID domain_id2qkmG00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id2qkmH01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1050 — Dcp2, box A domain
Domain ID domain_id2qkmH02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily10 — Nucleoside Triphosphate Pyrophosphohydrolase
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7. Citations (1)