SAXSdb — 1t6y

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

riboflavin kinase/FMN adenylyltransferase

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE-5'-DIPHOSPHATE × 2 ADENOSINE MONOPHOSPHATE × 2 FLAVIN MONONUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WZW1_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–293； UniProt 1–293 Author chain B； PDBConstruct 1–293； UniProt 1–293

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	1t6y
Deposition date deposition_date	2004-05-07
Structure title title	Crystal structure of ADP, AMP, and FMN bound TM379
Keywords keywords	;Crystal; FAD Synthetase; ADP; AMP; FMN; X-ray crystallography; Structural Genomics, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center, SIGNALING PROTEIN, TRANSFERASE ;; SIGNALING PROTEIN,TRANSFERASE
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.

1t6y__assembly_1__model_1

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

Download this curve (.dat)

1t6y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1t6y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.40 Å
Rg (electron density)	27.49 Å
Total Rg	28.26 Å
Atom count	4527
Residues	538
Excluded volume	80859 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1t6y__assembly_1__model_1`	dimeric （2）	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	riboflavin kinase/FMN adenylyltransferase
Molecular weight formula_weight	33665.8 kDa
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	4560

MVVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVHKDREFGRKLGFPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGFRPTVGDARNVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKKFDSIEELKAAIDQDVKSARNMIDDIINSKFEKEG

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1t6ya1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.5 — Riboflavin kinase-like
Family Family family	b.43.5.1 — ATP-dependent riboflavin kinase-like

Domain ID domain_id	d1t6ya2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.3 — Adenylyltransferase

Domain ID domain_id	d1t6yb1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.5 — Riboflavin kinase-like
Family Family family	b.43.5.1 — ATP-dependent riboflavin kinase-like

Domain ID domain_id	d1t6yb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.3 — Adenylyltransferase

CATH v4.4 (4 domains)

Domain ID domain_id	1t6yA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1t6yA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	30 — Riboflavin kinase-like

Domain ID domain_id	1t6yB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1t6yB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	30 — Riboflavin kinase-like

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Unit-cell length a length_a	67.803 Å
Unit-cell length b length_b	82.661 Å
Unit-cell length c length_c	66.717 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	0.2311
R_work r_work	0.2310
R_free r_free	0.2980

Crystal structure of ADP, AMP, and FMN bound TM379

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

riboflavin kinase/FMN adenylyltransferase

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

1t6y__assembly_1__model_1

1t6y__assembly_1__model_1 | I(q)

1t6y__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of ADP, AMP, and FMN bound TM379

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

riboflavin kinase/FMN adenylyltransferase

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

1t6y__assembly_1__model_1

1t6y__assembly_1__model_1 | I(q)

1t6y__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)