4qdv

Dcps in complex with covalent ligand

Method: X-RAY DIFFRACTION

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

m7GpppX diphosphatase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	4-{[(2,4-diaminoquinazolin-5-yl)oxy]methyl}benzenesulfonic acid × 1 PHOSPHATE ION × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	4-{[(2,4-diaminoquinazolin-5-yl)oxy]methyl}benzenesulfonic acid × 1 PHOSPHATE ION × 4 GLYCEROL × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCPS_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–337； UniProt 2–337 Author chain B； PDBConstruct 2–337； UniProt 2–337 Author chain C； PDBConstruct 2–337； UniProt 2–337 Author chain D； PDBConstruct 2–337； UniProt 2–337

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	4qdv
Deposition date deposition_date	2014-05-14
Structure title title	Dcps in complex with covalent ligand
Keywords keywords	Decapping scavenger enzyme, 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.

4qdv__assembly_1__model_1

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

Download this curve (.dat)

4qdv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4qdv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.16 Å
Rg (electron density)	25.09 Å
Total Rg	25.97 Å
Atom count	4827
Residues	575
Excluded volume	85474 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4qdv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4qdv__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 (4)

Entity 1 Entity 1 polymer

Description description	m7GpppX diphosphatase
Molecular weight formula_weight	38588.6 kDa
EC 编号 ec_number	3.6.1.59
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9697

GADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS

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 non-polymer

Description description	4-{[(2,4-diaminoquinazolin-5-yl)oxy]methyl}benzenesulfonic acid
Molecular weight formula_weight	346.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4qdva1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.246 — mRNA decapping enzyme DcpS N-terminal domain
Superfamily Superfamily superfamily	d.246.1 — mRNA decapping enzyme DcpS N-terminal domain
Family Family family	d.246.1.0 — automated matches

Domain ID domain_id	d4qdva2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.13 — HIT-like
Superfamily Superfamily superfamily	d.13.1 — HIT-like
Family Family family	d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain

Domain ID domain_id	d4qdvb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.246 — mRNA decapping enzyme DcpS N-terminal domain
Superfamily Superfamily superfamily	d.246.1 — mRNA decapping enzyme DcpS N-terminal domain
Family Family family	d.246.1.0 — automated matches

Domain ID domain_id	d4qdvb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.13 — HIT-like
Superfamily Superfamily superfamily	d.13.1 — HIT-like
Family Family family	d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain

Domain ID domain_id	d4qdvc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.246 — mRNA decapping enzyme DcpS N-terminal domain
Superfamily Superfamily superfamily	d.246.1 — mRNA decapping enzyme DcpS N-terminal domain
Family Family family	d.246.1.0 — automated matches

Domain ID domain_id	d4qdvc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.13 — HIT-like
Superfamily Superfamily superfamily	d.13.1 — HIT-like
Family Family family	d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain

Domain ID domain_id	d4qdvd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.246 — mRNA decapping enzyme DcpS N-terminal domain
Superfamily Superfamily superfamily	d.246.1 — mRNA decapping enzyme DcpS N-terminal domain
Family Family family	d.246.1.0 — automated matches

Domain ID domain_id	d4qdvd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.13 — HIT-like
Superfamily Superfamily superfamily	d.13.1 — HIT-like
Family Family family	d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain

CATH v4.4 (10 domains)

Domain ID domain_id	4qdvA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	40 — Scavenger mRNA decapping enzyme, N-terminal domain

Domain ID domain_id	4qdvA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	428 — HIT family, subunit A
Homologous superfamily homologous superfamily	10 — HIT-like

Domain ID domain_id	4qdvB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	40 — Scavenger mRNA decapping enzyme, N-terminal domain

Domain ID domain_id	4qdvB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2240 — mRNA decapping enzyme DcpS N-terminal fold
Homologous superfamily homologous superfamily	10 — mRNA decapping enzyme DcpS N-terminal domain

Domain ID domain_id	4qdvB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	428 — HIT family, subunit A
Homologous superfamily homologous superfamily	10 — HIT-like

Domain ID domain_id	4qdvC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	40 — Scavenger mRNA decapping enzyme, N-terminal domain

Domain ID domain_id	4qdvC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2240 — mRNA decapping enzyme DcpS N-terminal fold
Homologous superfamily homologous superfamily	10 — mRNA decapping enzyme DcpS N-terminal domain

Domain ID domain_id	4qdvC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	428 — HIT family, subunit A
Homologous superfamily homologous superfamily	10 — HIT-like

Domain ID domain_id	4qdvD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	40 — Scavenger mRNA decapping enzyme, N-terminal domain

Domain ID domain_id	4qdvD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	428 — HIT family, subunit A
Homologous superfamily homologous superfamily	10 — HIT-like

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Unit-cell length a length_a	101.090 Å
Unit-cell length b length_b	105.510 Å
Unit-cell length c length_c	140.000 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	84.260 Å
R factor r_factor	0.2078
R_work r_work	0.2055
R_free r_free	0.2499

Dcps in complex with covalent ligand

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

m7GpppX diphosphatase

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

4qdv__assembly_1__model_1

4qdv__assembly_1__model_1 | I(q)

4qdv__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Dcps in complex with covalent ligand

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

m7GpppX diphosphatase

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

4qdv__assembly_1__model_1

4qdv__assembly_1__model_1 | I(q)

4qdv__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. Citations (1)