3gd7

Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP)

Method: X-RAY DIFFRACTION

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

;Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371 ;

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ; × 1 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ; × 1 water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ; × 1 water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ; × 1 water × 1	Consistent with protein count
5	Insufficient information	Homooligomer	Protein 4	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ; × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CFTR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–237； UniProt 1193–1427 Author chain B； PDBConstruct 3–237； UniProt 1193–1427 Author chain C； PDBConstruct 3–237； UniProt 1193–1427 Author chain D； PDBConstruct 3–237； UniProt 1193–1427

;Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371 ;

Escherichia coli K-12

UniProt P68187

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ; × 1 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ; × 1 water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ; × 1 water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ; × 1 water × 1	Consistent with protein count
5	Insufficient information	Homooligomer	Protein 4	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ; × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 238–390； UniProt 219–371 Author chain B； PDBConstruct 238–390； UniProt 219–371 Author chain C； PDBConstruct 238–390； UniProt 219–371 Author chain D； PDBConstruct 238–390； UniProt 219–371

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	3gd7
Deposition date deposition_date	2009-02-23
Structure title title	Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP)
Keywords keywords	;CFTR, ABC transporter, nucleotide binding domain, NBD, ATP, P-ATP, N6-Phenylethyl-ATP, ATP-binding, Chloride channel, Ion transport, Ionic channel, Transport, Cell inner membrane, Cell membrane, Hydrolase, Sugar transport ;; 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.

3gd7__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3gd7__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gd7__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	38.22 Å
Rg (electron density)	37.61 Å
Total Rg	37.93 Å
Atom count	11580
Residues	1506
Excluded volume	206080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gd7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gd7__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3gd7__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3gd7__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3gd7__assembly_5__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	;Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371 ;
Molecular weight formula_weight	43518.8 kDa
Mutation mutation	Q1280E, Y1307N, E1308A, Q1309A, W1310H, H1402A, Q1411D
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	11834

SLIENSHVKKDDIWPSGGQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRLLNTEGEIQIDGVSWDSITLEQWRKAFGVIPQKVFIFSGTFRKNLDPNAAHSDQEIWKVADEVGLRSVIEQFPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPVTYQIIRRTLKQAFADCTVILCEARIEAMLECDQFLVIEENKVRQYDSILELYHYPADRFVAGFIGSPKMNFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGTACRRLHKEPGV

Source Source

Source organism organism	Escherichia coli K-12
Common name common_name	human,bacteria
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) ;
Molecular weight formula_weight	611.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	254

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3gd7A01
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	3gd7A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	3gd7A03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3gd7B01
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	3gd7B02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	3gd7B03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3gd7C01
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	3gd7C02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	3gd7C03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3gd7D01
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	3gd7D02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	3gd7D03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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Unit-cell length a length_a	137.837 Å
Unit-cell length b length_b	173.725 Å
Unit-cell length c length_c	82.574 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	54.000 Å
R factor r_factor	—
R_work r_work	0.2470
R_free r_free	0.3080

Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP)

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

;Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371 ;

State in the Current Structure

Other States of the Same Protein in the Database

;Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371 ;

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

3gd7__assembly_5__model_1

3gd7__assembly_5__model_1 | I(q)

3gd7__assembly_5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP)

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

;Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371 ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371 ;

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

3gd7__assembly_5__model_1

3gd7__assembly_5__model_1 | I(q)

3gd7__assembly_5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)