SAXSdb — 5ldd

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

Mon1

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ccz1 × 1 （G0SD94） Rab small monomeric GTPase-like protein × 1 （G0SGE1） SULFATE ION × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ccz1 × 1 （G0SD94） Rab small monomeric GTPase-like protein × 1 （G0SGE1） SULFATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0SGS3_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–166； UniProt 195–355 Author chain D； PDBConstruct 6–166； UniProt 195–355

Ccz1

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

UniProt G0SD94

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Mon1 × 1 （G0SGS3） Rab small monomeric GTPase-like protein × 1 （G0SGE1） SULFATE ION × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Mon1 × 1 （G0SGS3） Rab small monomeric GTPase-like protein × 1 （G0SGE1） SULFATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0SD94_CHATD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–250； UniProt 1–249 Author chain E； PDBConstruct 2–250； UniProt 1–249

Rab small monomeric GTPase-like protein

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

UniProt G0SGE1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Mon1 × 1 （G0SGS3） Ccz1 × 1 （G0SD94） SULFATE ION × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Mon1 × 1 （G0SGS3） Ccz1 × 1 （G0SD94） SULFATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0SGE1_CHATD
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–207； UniProt 1–205 Author chain F； PDBConstruct 3–207； UniProt 1–205

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	5ldd
Deposition date deposition_date	2016-06-24
Structure title title	Crystal structure of the heterodimeric GEF Mon1-Ccz1 in complex with Ypt7
Keywords keywords	heterodimeric GEF protein, endosomal maturation, Rab GTPase, protein transport; PROTEIN TRANSPORT
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.

5ldd__assembly_1__model_1

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

Download this curve (.dat)

5ldd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ldd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.55 Å
Rg (electron density)	25.38 Å
Total Rg	26.30 Å
Atom count	3869
Residues	489
Excluded volume	69387 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ldd__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ldd__assembly_2__model_1`	trimeric （3）	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	Mon1
Molecular weight formula_weight	18259.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	7670

GPLGSMEGFERELDNIPDTLPDDERLALWKGKLKHYLILSSAGKPIWSRHGDLSLVNSTMGVVQTIISFYEGARNPLLGFTAGKVRFVILIKGPLYFVAISRLRESDAQLRAQLEALYMQILSTLTLPILTNIFAHRPSTDLRGPLQGTESLLASLADSFTKGSPS

Source Source

Source organism organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ccz1
Molecular weight formula_weight	27657.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SMTTPVSPSPSGIIPAQLGFLAIYNPALGTTDETLEDQIVYYATASTLSQARRRHRRPRRRDRQRAQSVVKDSRPNAAGATGDSEAVAEDKDPVSKEERHERLRQIGLAQGMVEFAKSFSDGEPVDTIDTEKARVILVEVEEGWWILASIDLTRLPLPQIKTPTSSSAPPPAPNLNPLPPEPAYEYSSREVKPPSLLRADLLRAYDLFLLHHGSSLSSLLASQGRAQLVASLTRFWDHFLATWNVLLHGN

Source Source

Source organism organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Rab small monomeric GTPase-like protein
Molecular weight formula_weight	23218.2 kDa
Mutation mutation	N125I
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

GSMSSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSASYKATIGADFLTREVMVDDRQVTMQLWDTAGQERFQSLGVAFYRGADCCVLVFDVNNAKSFDALDSWRDEFLIQASPRDPENFPFVVLGIKIDVEESKRVISTKRAQTFCQSKGGIPYFETSAKEAINVEEAFQVIARNALMQEESEEFSGDFQDPINIHIENERDGCAC

Source Source

Source organism organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	122

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5lddc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d5lddf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5lddC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5lddF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	70.083 Å
Unit-cell length b length_b	103.812 Å
Unit-cell length c length_c	206.667 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.496 Å
Low-resolution limit resolution_low	46.380 Å
R factor r_factor	0.2016
R_work r_work	0.2000
R_free r_free	0.2411

Crystal structure of the heterodimeric GEF Mon1-Ccz1 in complex with Ypt7

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

Mon1

State in the Current Structure

Other States of the Same Protein in the Database

Ccz1

State in the Current Structure

Other States of the Same Protein in the Database

Rab small monomeric GTPase-like protein

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

5ldd__assembly_1__model_1

5ldd__assembly_1__model_1 | I(q)

5ldd__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

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the heterodimeric GEF Mon1-Ccz1 in complex with Ypt7

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

Mon1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ccz1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Rab small monomeric GTPase-like protein

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

5ldd__assembly_1__model_1

5ldd__assembly_1__model_1 | I(q)

5ldd__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

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)