SAXSdb — 6wv5

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

Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein

Aequorea victoria

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	(2R,3R)-2-hydroxy-3-methyl-2-[(2E,7S)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-2,3-dihydronaphthalene-1,4-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A059PIQ0_AEQVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–142； UniProt 1–144 Author chain A； PDBConstruct 296–381； UniProt 146–231

Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein

Aequorea victoria

UniProt Q9BQB6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	(2R,3R)-2-hydroxy-3-methyl-2-[(2E,7S)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-2,3-dihydronaphthalene-1,4-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VKOR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 143–295； UniProt 3–155

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	6wv5
Deposition date deposition_date	2020-05-05
Structure title title	Human VKOR C43S mutant with vitamin K1 epoxide
Keywords keywords	;Vitamin K epoxide Reductase (VKOR), Vitamin K, warfarin, superwarfarin, vitamin K expoxide(KO), membrane protein, OXIDOREDUCTASE, FLUORESCENT PROTEIN ;; OXIDOREDUCTASE, FLUORESCENT PROTEIN
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.

6wv5__assembly_1__model_1

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

Download this curve (.dat)

6wv5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wv5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.41 Å
Rg (electron density)	27.00 Å
Total Rg	27.50 Å
Atom count	2992
Residues	370
Excluded volume	52884 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wv5__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 (2)

Entity 1 Entity 1 polymer

Description description	Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein
Molecular weight formula_weight	44181.4 kDa
EC 编号 ec_number	1.17.4.4
Mutation mutation	C43S
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	2992

MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLXVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNSTWGSPGWVRLALCLTGLVLSLYALHVKAARARDRDYRALSDVGTAISCSRVFSSRWGRGFGLVEHVLGQDSILNQSNSIFGCIFYTLQLLLGCLRTRWASVLMLLSSLVSLAGSVYLAWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQENSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHHHHHHHHHH

Source Source

Source organism organism	Aequorea victoria
Common name common_name	Jellyfish
NCBI taxonomy ID ncbi_taxonomy_id	6100
Host organism host_organism	Komagataella pastoris

Entity 2 Entity 2 non-polymer

Description description	(2R,3R)-2-hydroxy-3-methyl-2-[(2E,7S)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-2,3-dihydronaphthalene-1,4-dione
Molecular weight formula_weight	468.7 kDa
Source method src_method	man
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6wv5A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	130 — VKOR domain

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Unit-cell length a length_a	88.927 Å
Unit-cell length b length_b	88.927 Å
Unit-cell length c length_c	229.889 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	9

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	39.478 Å
R factor r_factor	0.2331
R_work r_work	0.2311
R_free r_free	0.2704

Human VKOR C43S mutant with vitamin K1 epoxide

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

Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein

State in the Current Structure

Other States of the Same Protein in the Database

Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein

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

6wv5__assembly_1__model_1

6wv5__assembly_1__model_1 | I(q)

6wv5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (2)

Human VKOR C43S mutant with vitamin K1 epoxide

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

Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein

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

6wv5__assembly_1__model_1

6wv5__assembly_1__model_1 | I(q)

6wv5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (2)