SAXSdb — 6qv2

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

ABC transporter, ATP-binding protein

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Uncharacterized ABC transporter ATP-binding protein TM_0288 × 1 （Q9WYC4） Nb_TM No.2 × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Uncharacterized ABC transporter ATP-binding protein TM_0288 × 1 （Q9WYC4） Nb_TM No.2 × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WYC3_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–587； UniProt 2–577 Author chain C； PDBConstruct 12–587； UniProt 2–577

Uncharacterized ABC transporter ATP-binding protein TM_0288

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

UniProt Q9WYC4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	ABC transporter, ATP-binding protein × 1 （Q9WYC3） Nb_TM No.2 × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	ABC transporter, ATP-binding protein × 1 （Q9WYC3） Nb_TM No.2 × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y288_THEMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–598； UniProt 1–598 Author chain D； PDBConstruct 1–598； UniProt 1–598

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	6qv2
Deposition date deposition_date	2019-03-01
Structure title title	Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2
Keywords keywords	ABC exporter, ABC transporter, Membrane Transporter, MEMBRANE PROTEIN, nanobody; MEMBRANE PROTEIN
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.

6qv2__assembly_1__model_1

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

Download this curve (.dat)

6qv2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6qv2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.32 Å
Rg (electron density)	38.85 Å
Total Rg	39.23 Å
Atom count	10043
Residues	1267
Excluded volume	181460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6qv2__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6qv2__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	ABC transporter, ATP-binding protein
Molecular weight formula_weight	65016.8 kDa
Mutation mutation	D41A
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	20086

GPSGSGGGGGSKTLARYLKPYWIFAVLAPLFMVVEVICDLSQPTLLARIVAEGIARGDFSLVLKTGILMLIVALIGAVGGIGCTVFASYASQNFGADLRRDLFRKVLSFSISNVNRFHTSSLITRLTNDVTQLQNLVMMLLRIVVRAPLLFVGGIVMAVSINVKLSSVLIFLIPPIVLLFVWLTKKGNPLFRKIQESTDEVNRVVRENLLGVRVVRAFRREEYENENFRKANESLRRSIISAFSLIVFALPLFIFIVNMGMIAVLWFGGVLVRNNQMEIGSIMAYTNYLMQIMFSLMMIGNILNFIVRASASAKRVLEVLNEKPAIEEADNALALPNVEGSVSFENVEFRYFENTDPVLSGVNFSVKPGSLVAVLGETGSGKSTLMNLIPRLIDPERGRVEVDELDVRTVKLKDLRGHISAVPQETVLFSGTIKENLKWGREDATDDEIVEAAKIAQIHDFIISLPEGYDSRVERGGRNFSGGQKQRLSIARALVKKPKVLILDDCTSSVDPITEKRILDGLKRYTKGCTTFIITQKIPTALLADKILVLHEGKVAGFGTHKELLEHCKPYREIYESQFGNGVMNDA

Source Source

Source organism organism	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Uncharacterized ABC transporter ATP-binding protein TM_0288
Molecular weight formula_weight	67758.9 kDa
Mutation mutation	D65A, E517A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MPEIRRRPHGPILEKPALKNPTATLRRLLGYLRPHTFTLIMVFVFVTVSSILGVLSPYLIGKTIAVVFVPRRFDLLPRYMLILGTIYALTSLLFWLQGKIMLTLSQDVVFRLRKELFEKLQRVPVGFFDRTPHGDIISRVINDVDNINNVLGNSIIQFFSGIVTLAGAVIMMFRVNVILSLVTLSIVPLTVLITQIVSSQTRKYFYENQRVLGQLNGIIEEDISGLTVIKLFTREEKEMEKFDRVNESLRKVGTKAQIFSGVLPPLMNMVNNLGFALISGFGGWLALKDIITVGTIATFIGYSRQFTRPLNELSNQFNMIQMALASAERIFEILDLEEEKDDPDAVELREVRGEIEFKNVWFSYDKKKPVLKDITFHIKPGQKVALVGPTGSGKTTIVNLLMRFYDVDRGQILVDGIDIRKIKRSSLRSSIGIVLQDTILFSTTVKENLKYGNPGATDEEIKEAAKLTHSDHFIKHLPEGYETVLTDNGEDLSQGQRQLLAITRAFLANPKILILDAATSNVDTKTEKSIQAAMWKLMEGKTSIIIAHRLNTIKNADLIIVLRDGEIVEMGKHDELIQKRGFYYELFTSQYGLVVEKEA

Source Source

Source organism organism	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nb_TM No.2
Molecular weight formula_weight	14131.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPSQGQLVESGGGLVQPGGSLRLSCAASGFTLDYYAIGWFRQAPGKEREGVSCISNSGGSTKYADSVKGRFTISRDKAKNTVYLQMNSLKPEDTGVYYCAADRGYSEYDLPCDLVIYGMDYWGKGTPVTVSA

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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Unit-cell length a length_a	88.600 Å
Unit-cell length b length_b	113.070 Å
Unit-cell length c length_c	126.890 Å
Unit-cell angle α angle_alpha	83.18 °
Unit-cell angle β angle_beta	73.00 °
Unit-cell angle γ angle_gamma	67.37 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.230 Å
Low-resolution limit resolution_low	32.590 Å
R factor r_factor	0.3070
R_work r_work	0.3060
R_free r_free	0.3300

Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2

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

ABC transporter, ATP-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

Uncharacterized ABC transporter ATP-binding protein TM_0288

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

6qv2__assembly_1__model_1

6qv2__assembly_1__model_1 | I(q)

6qv2__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 non-polymer

7. Citations (1)

Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2

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

ABC transporter, ATP-binding 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

Uncharacterized ABC transporter ATP-binding protein TM_0288

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

6qv2__assembly_1__model_1

6qv2__assembly_1__model_1 | I(q)

6qv2__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 non-polymer

7. Citations (1)