SAXSdb — 2frd

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

NAD(P) transhydrogenase subunit alpha part 1

Rhodospirillum rubrum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	NAD(P) transhydrogenase subunit beta × 1 （Q59765） 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PNTAA_RHORU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–384； UniProt 1–384 Author chain B； PDBConstruct 1–384； UniProt 1–384

NAD(P) transhydrogenase subunit beta

Rhodospirillum rubrum

UniProt Q59765

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	NAD(P) transhydrogenase subunit alpha part 1 × 2 （Q60164） 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PNTB_RHORU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–203； UniProt 262–464

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	2frd
Deposition date deposition_date	2006-01-19
Structure title title	Structure of Transhydrogenase (dI.S138A.NADH)2(dIII.NADPH)1 asymmetric complex
Keywords keywords	NAD(P) TRANSHYDROGENASE SUBUNITS, NADH, NADPH, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

2frd__assembly_1__model_1

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

Download this curve (.dat)

2frd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2frd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.27 Å
Rg (electron density)	30.61 Å
Total Rg	31.29 Å
Atom count	6755
Residues	896
Excluded volume	121550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2frd__assembly_1__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	NAD(P) transhydrogenase subunit alpha part 1
Molecular weight formula_weight	40308.8 kDa
EC 编号 ec_number	1.6.1.2
Mutation mutation	S138A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6758

MKIAIPKERRPGEDRVAISPEVVKKLVGLGFEVIVEQGAGVGASITDDALTAAGATIASTAAQALSQADVVWKVQRPMTAEEGTDEVALIKEGAVLMCHLGALTNRPVVEALTKRKITAYAMELMPRISRAQSMDILASQSNLAGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVDDEAMKTAETAGGYAKEMGEEFRKKQAEAVLKELVKTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVPSRVAADASPLFAKNLLNFLTPHVDKDTKTLVMKLEDETVSGTCVTRDGAIVHPALTGQGA

Source Source

Source organism organism	Rhodospirillum rubrum
NCBI taxonomy ID ncbi_taxonomy_id	1085
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	NAD(P) transhydrogenase subunit beta
Molecular weight formula_weight	21485.5 kDa
EC 编号 ec_number	1.6.1.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MNRSIFNVILGGFGSEGGVAAAGGAAGDRSVKAGSAEDAAFIMKNASKVIIVPGYGMAVAQAQHALREMADVLKKEGVEVSYAIHPVAGRMPGHMNVLLAEANVPYDEVFELEEINSSFQTADVAFVIGANDVTNPAAKTDPSSPIYGMPILDVEKAGTVLFIKRSMASGYAGVENELFFRNNTMMLFGDAKKMTEQIVQAMN

Source Source

Source organism organism	Rhodospirillum rubrum
NCBI taxonomy ID ncbi_taxonomy_id	1085
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2frda1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain

Domain ID domain_id	d2frda2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
Family Family family	c.23.12.2 — L-alanine dehydrogenase-like

Domain ID domain_id	d2frdb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain

Domain ID domain_id	d2frdb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
Family Family family	c.23.12.2 — L-alanine dehydrogenase-like

Domain ID domain_id	d2frdc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.4 — Transhydrogenase domain III (dIII)

CATH v4.4 (5 domains)

Domain ID domain_id	2frdA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2frdA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2frdB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2frdB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2frdC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

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Unit-cell length a length_a	71.300 Å
Unit-cell length b length_b	74.110 Å
Unit-cell length c length_c	205.220 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	3.200 Å
Low-resolution limit resolution_low	45.930 Å
R factor r_factor	0.2185
R_work r_work	0.2134
R_free r_free	0.2723

Structure of Transhydrogenase (dI.S138A.NADH)2(dIII.NADPH)1 asymmetric complex

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

NAD(P) transhydrogenase subunit alpha part 1

State in the Current Structure

Other States of the Same Protein in the Database

NAD(P) transhydrogenase subunit beta

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

2frd__assembly_1__model_1

2frd__assembly_1__model_1 | I(q)

2frd__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Structure of Transhydrogenase (dI.S138A.NADH)2(dIII.NADPH)1 asymmetric complex

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

NAD(P) transhydrogenase subunit alpha part 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NAD(P) transhydrogenase subunit beta

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

2frd__assembly_1__model_1

2frd__assembly_1__model_1 | I(q)

2frd__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)