1xmm

Structure of human Dcps bound to m7GDP

Method: X-RAY DIFFRACTION

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

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein homooligomer	Homooligomer	2 / 0 / 0 / 0	Consistent with protein count
2	Protein homooligomer	Homooligomer	2 / 0 / 0 / 0	Consistent with protein count

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	1xmm
Deposition date deposition_date	2004-10-04
Structure title title	Structure of human Dcps bound to m7GDP
Keywords keywords	scavenger decapping enzyme bound m7GDP, CHAPERONE; CHAPERONE
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.

1xmm__assembly_1__model_1

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

Download this curve (.dat)

1xmm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xmm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.95 Å
Rg (electron density)	24.87 Å
Total Rg	25.74 Å
Atom count	4825
Residues	575
Excluded volume	85690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xmm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xmm__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 (5)

Entity 1 Entity 1 polymer

Description description	heat shock-like protein 1
Molecular weight formula_weight	39074.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C,D
Atom count atom_count	10108

GPLGSMADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	378.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	458.2 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	419

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1xmma1
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	d1xmma2
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	d1xmmb1
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	d1xmmb2
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	d1xmmc1
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	d1xmmc2
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	d1xmmd1
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	d1xmmd2
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

CATH v4.4 (10 domains)

Domain ID domain_id	1xmmA01
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	1xmmA02
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	1xmmB01
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	1xmmB02
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	1xmmB03
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	1xmmC01
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	1xmmC02
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	1xmmC03
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	1xmmD01
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	1xmmD02
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	100.928 Å
Unit-cell length b length_b	105.140 Å
Unit-cell length c length_c	138.647 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	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2162
R_work r_work	0.2135
R_free r_free	0.2670