SAXSdb — 1og6

▼

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

HYPOTHETICAL OXIDOREDUCTASE YDHF

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YDHF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–298； UniProt 1–298 Author chain B； PDBConstruct 1–298； UniProt 1–298 Author chain C； PDBConstruct 1–298； UniProt 1–298

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1og6
Deposition date deposition_date	2003-04-24
Structure title title	ydhF, an aldo-keto reductase from E.coli complexed with NADPH
Keywords keywords	;OXIDOREDUCTASE, ALDO-KETO REDUCTASE, ALPHA/BETA BARREL, NADPH-DEPENDANT, BACTERIAL TARGETS AT IGS-CNRS, FRANCE, BIGS, STRUCTURAL GENOMICS ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1og6__assembly_1__model_1

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

Download this curve (.dat)

1og6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1og6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.07 Å
Rg (electron density)	30.93 Å
Total Rg	31.68 Å
Atom count	7224
Residues	890
Excluded volume	127970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1og6__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HYPOTHETICAL OXIDOREDUCTASE YDHF
Molecular weight formula_weight	33648.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7423

LVQRITIAPQGPEFSRFVMGYWRLMDWNMSARQLVSFIEEHLDLGVTTVDHADIYGGYQCEAAFGEALKLAPHLRERMEIVSKCGIATTAREENVIGHYITDRDHIIKSAEQSLINLATDHLDLLLIHRPDPLMDADEVADAFKHLHQSGKVRHFGVSNFTPAQFALLQSRLPFTLATNQVEISPVHQPLLLDGTLDQLQQLRVRPMAWSCLGGGRLFNDDYFQPLRDELAVVAEELNAGSIEQVVNAWVLRLPSQPLPIIGSGKIERVRAAVEAETLKMTRQQWFRIRKAALGYDVP

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 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	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	199

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1og6a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.7 — NAD(P)-linked oxidoreductase
Family Family family	c.1.7.1 — Aldo-keto reductases (NADP)

Domain ID domain_id	d1og6b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.7 — NAD(P)-linked oxidoreductase
Family Family family	c.1.7.1 — Aldo-keto reductases (NADP)

Domain ID domain_id	d1og6c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.7 — NAD(P)-linked oxidoreductase
Family Family family	c.1.7.1 — Aldo-keto reductases (NADP)

CATH v4.4 (3 domains)

Domain ID domain_id	1og6A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	100 — NADP-dependent oxidoreductase domain

Domain ID domain_id	1og6B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	100 — NADP-dependent oxidoreductase domain

Domain ID domain_id	1og6C00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	100 — NADP-dependent oxidoreductase domain

▶

Unit-cell length a length_a	174.529 Å
Unit-cell length b length_b	174.529 Å
Unit-cell length c length_c	97.923 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	27

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	29.910 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2380

ydhF, an aldo-keto reductase from E.coli complexed with NADPH

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

HYPOTHETICAL OXIDOREDUCTASE YDHF

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

1og6__assembly_1__model_1

1og6__assembly_1__model_1 | I(q)

1og6__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 (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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

ydhF, an aldo-keto reductase from E.coli complexed with NADPH

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

HYPOTHETICAL OXIDOREDUCTASE YDHF

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

1og6__assembly_1__model_1

1og6__assembly_1__model_1 | I(q)

1og6__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 (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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)