SAXSdb — 1ye6

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

NAD(P)H-dependent D-xylose reductase

Candida tenuis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 8	SULFATE ION × 16 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 water × 8	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 8 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 4	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 8 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XYL1_CANTE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–322； UniProt 1–322 Author chain B； PDBConstruct 1–322； UniProt 1–322 Author chain C； PDBConstruct 1–322； UniProt 1–322 Author chain D； PDBConstruct 1–322； UniProt 1–322

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	1ye6
Deposition date deposition_date	2004-12-28
Structure title title	Crystal structure of the Lys-274 to Arg mutant of Candida tenuis xylose reductase (AKR2B5) bound to NADP+
Keywords keywords	beta-alpha-barrel AKR aldo-keto reductase coenzyme specificity NADP, 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.

1ye6__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ye6__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ye6__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	41.57 Å
Rg (electron density)	41.25 Å
Total Rg	41.47 Å
Atom count	10356
Residues	1276
Excluded volume	184900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ye6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ye6__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1ye6__assembly_3__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1ye6__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1ye6__assembly_5__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 (5)

Entity 1 Entity 1 polymer

Description description	NAD(P)H-dependent D-xylose reductase
Molecular weight formula_weight	36090.2 kDa
EC 编号 ec_number	1.1.1.-
Mutation mutation	K274R
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	11116

MSASIPDIKLSSGHLMPSIGFGCWKLANATAGEQVYQAIKAGYRLFDGAEDYGNEKEVGDGVKRAIDEGLVKREEIFLTSKLWNNYHDPKNVETALNKTLADLKVDYVDLFLIHFPIAFKFVPIEEKYPPGFYCGDGNNFVYEDVPILETWKALEKLVAAGKIKSIGVSNFPGALLLDLLRGATIKPAVLQVEHHPYLQQPKLIEFAQKAGVTITAYSSFGPQSFVEMNQGRALNTPTLFAHDTIKAIAAKYNKTPAEVLLRWAAQRGIAVIPRSNLPERLVQNRSFNTFDLTKEDFEEIAKLDIGLRFNDPWDWDNIPIFV

Source Source

Source organism organism	Candida tenuis
NCBI taxonomy ID ncbi_taxonomy_id	45596
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

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	2

Entity 4 Entity 4 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 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	760

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ye6a_
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	d1ye6b_
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	d1ye6c_
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	d1ye6d_
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 (4 domains)

Domain ID domain_id	1ye6A00
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	1ye6B00
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	1ye6C00
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	1ye6D00
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

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Unit-cell length a length_a	180.005 Å
Unit-cell length b length_b	127.988 Å
Unit-cell length c length_c	80.074 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2290

Crystal structure of the Lys-274 to Arg mutant of Candida tenuis xylose reductase (AKR2B5) bound to NADP+

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

NAD(P)H-dependent D-xylose 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

1ye6__assembly_5__model_1

1ye6__assembly_5__model_1 | I(q)

1ye6__assembly_5__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 the Lys-274 to Arg mutant of Candida tenuis xylose reductase (AKR2B5) bound to NADP+

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

NAD(P)H-dependent D-xylose 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

1ye6__assembly_5__model_1

1ye6__assembly_5__model_1 | I(q)

1ye6__assembly_5__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)