SAXSdb — 9vcn

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

NADH-dependent dihydrogenase

Amycolatopsis mediterranei S699

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RifT × 2 （O52542） ;(7E,9S,10S,11R,12R,13R,14R,15R,16S,17S,18E,20Z)-2,4,10,12,14,16-hexahydroxy-3,7,9,11,13,15,17,21-octamethyl-23-azatricyclo[22.3.1.05,27]octacosa-1,3,5(27),7,18,20,24-heptaene-6,22,26,28-tetrone ; × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O52541_AMYMD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–342； UniProt 1–342 Author chain C； PDBConstruct 1–342； UniProt 1–342

RifT

Amycolatopsis mediterranei S699

UniProt O52542

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	NADH-dependent dihydrogenase × 2 （O52541） ;(7E,9S,10S,11R,12R,13R,14R,15R,16S,17S,18E,20Z)-2,4,10,12,14,16-hexahydroxy-3,7,9,11,13,15,17,21-octamethyl-23-azatricyclo[22.3.1.05,27]octacosa-1,3,5(27),7,18,20,24-heptaene-6,22,26,28-tetrone ; × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O52542_AMYMD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–256； UniProt 2–255 Author chain D； PDBConstruct 3–256； UniProt 2–255

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	9vcn
Deposition date deposition_date	2025-06-06
Last revision last_revision	2026-06-10
Structure title title	NAD-DEPENDENT DEHYDROGENASE
Keywords keywords	DEHYDROGENASE, COMPLEX, NAD-DEPENDENT, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC 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.

9vcn__assembly_1__model_1

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

Download this curve (.dat)

9vcn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vcn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.15 Å
Rg (electron density)	33.33 Å
Total Rg	33.98 Å
Atom count	8434
Residues	1151
Excluded volume	148190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vcn__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	NADH-dependent dihydrogenase
Molecular weight formula_weight	35368.6 kDa
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	8640

MAPTGGVGESRYVKTLRQLEVALIGAGLIARLHLEAWLGAGAAVRVYSDDGRSRELAAEFGAKAAGSLEEALDGADAVDICTPTASHHEIALTAIAAGVGVVCEKPLAASAEEAEEIVTAAERAGVRLYAAHDVRFAAPYARLHELVASGRLGEGALGRFSFSAYHPRPWTGHASARSGGILTDQLLHGADLAHWVFGDVVRVHACYQGDIATPAPEGAVATGTAVLTHASGAISQVVSRWTATPRPPVRVAFHVSGTGGSVSYDSEWPQEVRVVDGGAGNFAYGGPSVFDTEMREFATAFAGGPEPRIGAKDALAAVRIIHAAAESAWTGRAVELPVRGAA

Source Source

Source organism organism	Amycolatopsis mediterranei S699
NCBI taxonomy ID ncbi_taxonomy_id	713604
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RifT
Molecular weight formula_weight	26214.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MVKVAILSSTPQAYAGALRGLPDVEVVAAASWDAFEPVRQAAEAGARVLCEYPPAAKETDLKAMIDAAGDRLTFASPACHGEAFAVVRKGIADGGIGELTTVLGSVATSVDGVLGAAAPYLLDLADAVLGGEPAQQVYAQTNIVLSGRIGESAAVLTVRYRSGQVASFDCRRHGSATGLPAVTFIGDQGSVQYDAGPQLLGGERPELGGEDLEALMLKDFLGAGDGPGPDGQAALRTFRIIQAAYESAHTGQPVDL

Source Source

Source organism organism	Amycolatopsis mediterranei S699
NCBI taxonomy ID ncbi_taxonomy_id	713604
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	;(7E,9S,10S,11R,12R,13R,14R,15R,16S,17S,18E,20Z)-2,4,10,12,14,16-hexahydroxy-3,7,9,11,13,15,17,21-octamethyl-23-azatricyclo[22.3.1.05,27]octacosa-1,3,5(27),7,18,20,24-heptaene-6,22,26,28-tetrone ;
Molecular weight formula_weight	639.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	206

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Unit-cell length a length_a	190.854 Å
Unit-cell length b length_b	82.354 Å
Unit-cell length c length_c	88.277 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.390 Å
Low-resolution limit resolution_low	46.980 Å
R factor r_factor	0.1959
R_work r_work	0.1938
R_free r_free	0.2502

NAD-DEPENDENT DEHYDROGENASE

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

NADH-dependent dihydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

RifT

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

9vcn__assembly_1__model_1

9vcn__assembly_1__model_1 | I(q)

9vcn__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 (4)

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 water

7. Citations (1)

NAD-DEPENDENT DEHYDROGENASE

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

NADH-dependent dihydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RifT

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

9vcn__assembly_1__model_1

9vcn__assembly_1__model_1 | I(q)

9vcn__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 (4)

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 water

7. Citations (1)