SAXSdb — 6dfr

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

DIHYDROFOLATE REDUCTASE

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 NADP 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	DYR_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 1–159

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	6dfr
Deposition date deposition_date	1988-10-21
Structure title title	CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. THE NADP+ HOLOENZYME AND THE FOLATE(DOT)NADP+ TERNARY COMPLEX. SUBSTRATE BINDING AND A MODEL FOR THE TRANSITION STATE
Keywords keywords	OXIDO-REDUCTASE, 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.

6dfr__assembly_1__model_1

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

Download this curve (.dat)

6dfr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6dfr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.77 Å
Rg (electron density)	15.35 Å
Total Rg	16.31 Å
Atom count	1259
Residues	154
Excluded volume	22159 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6dfr__assembly_1__model_1`	monomeric （1）	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	DIHYDROFOLATE REDUCTASE
Molecular weight formula_weight	18020.3 kDa
EC 编号 ec_number	1.5.1.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1331

MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLDKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	72

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6dfra_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.1 — Dihydrofolate reductases

CATH v4.4 (1 domains)

Domain ID domain_id	6dfrA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

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7. Citations (13)

;Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state. ;

Biochemistry (1990)

PMID: 2185835 · DOI: 10.1021/bi00465a018 PRIMARY

Effect of Single Amino Acid Replacements on the Folding and Stability of Dihydrofolate Reductase from Escherichia Coli

Biochemistry (1987)

;Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. I. General Features and Binding of Methotrexate ;

J.Biol.Chem. (1982)

;Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. II. Environment of Bound Nadph and Implications for Catalysis ;

J.Biol.Chem. (1982)

Crystal Structure of Avian Dihydrofolate Reductase Containing Phenyltriazine and Nadph

J.Biol.Chem. (1982)

;Interpretation of Nuclear Magnetic Resonance Spectra for Lactobacillus Casei Dihydrofolate Reductase Based on the X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex ;

Biochemistry (1979)

Dihydrofolate Reductase from Lactobacillus Casei. Stereochemistry of Nadph Binding

J.Biol.Chem. (1979)

;Proton Magnetic Resonance Studies on Escherichia Coli Dihydrofolate Reductase. Assignment of Histidine C-2 Protons in Binary Complexes with Folates on the Basis of the Crystal Structure with Methotrexate and on Chemical Modifications ;

J.Biol.Chem. (1979)

Dihydrofolate Reductase. The Amino Acid Sequence of the Enzyme from a Methotrexate-Resistant Mutant of Escherichia Coli

Biochemistry (1978)

Dihydrofolate Reductase from Lactobacillus Casei. X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex

J.Biol.Chem. (1978)

Dihydrofolate Reductase. X-Ray Structure of the Binary Complex with Methotrexate

Science (1977)

Dihydrofolate Reductase. Purification and Characterization of the Enzyme from an Amethopterin-Resistant Mutant of Escherichia Coli

Biochemistry (1972)

;Crystal Structure of Unliganded Escherichia Coli Dihydrofolate Reductase. Ligand-Induced Conformational Changes and Cooperativity in Binding ;

To be Published

Unit-cell length a length_a	34.853 Å
Unit-cell length b length_b	59.000 Å
Unit-cell length c length_c	81.282 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1920
R_work r_work	—
R_free r_free	—

CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. THE NADP+ HOLOENZYME AND THE FOLATE(DOT)NADP+ TERNARY COMPLEX. SUBSTRATE BINDING AND A MODEL FOR THE TRANSITION STATE

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

DIHYDROFOLATE REDUCTASE

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

6dfr__assembly_1__model_1

6dfr__assembly_1__model_1 | I(q)

6dfr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (13)

CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. THE NADP+ HOLOENZYME AND THE FOLATE(DOT)NADP+ TERNARY COMPLEX. SUBSTRATE BINDING AND A MODEL FOR THE TRANSITION STATE

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

DIHYDROFOLATE REDUCTASE

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

6dfr__assembly_1__model_1

6dfr__assembly_1__model_1 | I(q)

6dfr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (13)