1o8c

CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH

Method: X-RAY DIFFRACTION

▼

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

YHDH

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YHDH_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–345； UniProt 2–324 Author chain B； PDBConstruct 23–345； UniProt 2–324 Author chain C； PDBConstruct 23–345； UniProt 2–324 Author chain D； PDBConstruct 23–345； UniProt 2–324

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	1o8c
Deposition date deposition_date	2002-11-26
Structure title title	CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH
Keywords keywords	STRUCTURAL GENOMICS, UNKNOWN FUNCTION, POSSIBLE NADPH-DEPENDENT QUINONE OXIDOREDUCTASE; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1o8c__assembly_1__model_1

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

Download this curve (.dat)

1o8c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1o8c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.75 Å
Rg (electron density)	28.11 Å
Total Rg	28.61 Å
Atom count	4976
Residues	648
Excluded volume	88334 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1o8c__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1o8c__assembly_2__model_1`	dimeric （2）	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	YHDH
Molecular weight formula_weight	37294.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10292

MSYYHHHHHHLESTSLYKKAGLQALLLEQQDGKTLASVQTLDESRLPEGDVTVDVHWSSLNYKDALAITGKGKIIRNFPMIPGIDFAGTVRTSEDPRFHAGQEVLLTGWGVGENHWGGLAEQARVKGDWLVAMPQGLDARKAMIIGTAGFTAMLCVMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGRESTHEYLKSLGASRVLPRDEFAESRPLEKQVWAGAIDTVGDKVLAKVLAQMNYGGCVAACGLAGGFTLPTTVMPFILRNVRLQGVDSVMTPPERRAQAWQRLVADLPESFYTQAAKEISLSEAPNFAEAIINNQIQGRTLVKVN

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	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	348

▼

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d1o8ca3
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1o8ca4
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.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1o8ca5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1o8cb3
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1o8cb4
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.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1o8cb5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1o8cc1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1o8cc3
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.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1o8cd3
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1o8cd4
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.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1o8cd5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	1o8cA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	1o8cA02
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	1o8cB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	1o8cB02
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	1o8cC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	1o8cC02
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	1o8cD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	1o8cD02
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

▶

Unit-cell length a length_a	189.313 Å
Unit-cell length b length_b	189.313 Å
Unit-cell length c length_c	98.654 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	24

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	158.110 Å
R factor r_factor	0.1730
R_work r_work	0.1710
R_free r_free	0.2020

CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH

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

YHDH

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

1o8c__assembly_1__model_1

1o8c__assembly_1__model_1 | I(q)

1o8c__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) 19 domains

SCOP 2.08 (11 domains)

CATH v4.4 (8 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH

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

YHDH

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

1o8c__assembly_1__model_1

1o8c__assembly_1__model_1 | I(q)

1o8c__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) 19 domains

SCOP 2.08 (11 domains)

CATH v4.4 (8 domains)

7. Citations (1)