SAXSdb — 6wvb

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

Vitamin K epoxide reductase-like protein, 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	S-WARFARIN × 1 water × 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 313–405； UniProt 146–238

Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein

Aequorea victoria

UniProt K0NYR4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	S-WARFARIN × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	K0NYR4_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–142； UniProt 1–144

Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein

Aequorea victoria

UniProt Q6TEK8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	S-WARFARIN × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6TEK8_TAKRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 143–312； UniProt 6–175

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	6wvb
Deposition date deposition_date	2020-05-05
Structure title title	Takifugu rubripes VKOR-like with warfarin
Keywords keywords	Vitamin K epoxide Reductase, VKOR, VKOR-like protein, VKORL, membrane protein; MEMBRANE 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.

6wvb__assembly_1__model_1

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

Download this curve (.dat)

6wvb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wvb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.99 Å
Rg (electron density)	27.42 Å
Total Rg	28.05 Å
Atom count	3251
Residues	408
Excluded volume	58404 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wvb__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 (3)

Entity 1 Entity 1 polymer

Description description	Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein
Molecular weight formula_weight	46782.6 kDa
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	3261

MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLXVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNLRVSTPRWERIARVLVCLLGILLSLYAFHVEREHARDPSYKALCDVSSSISCSKVFGSRWGRGFGLLGSIFGNDSALNQPNSVYGIVFYAFQLLLGMTVSAMAALILMTTSIMSVVGSLYLGYILYFVLKDLCVICVTTYALNFILFVLNYKRLVYLNEAWKQKLQAKQDNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGMDELYKSNSLEVLFQ

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	S-WARFARIN
Molecular weight formula_weight	308.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6wvbA01
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	65.503 Å
Unit-cell length b length_b	93.386 Å
Unit-cell length c length_c	162.973 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	2.872 Å
Low-resolution limit resolution_low	40.513 Å
R factor r_factor	0.2429
R_work r_work	0.2406
R_free r_free	0.2859

Takifugu rubripes VKOR-like with warfarin

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

Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein

State in the Current Structure

Other States of the Same Protein in the Database

Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein

State in the Current Structure

Other States of the Same Protein in the Database

Vitamin K epoxide reductase-like protein, 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

6wvb__assembly_1__model_1

6wvb__assembly_1__model_1 | I(q)

6wvb__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (2)

Takifugu rubripes VKOR-like with warfarin

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

Vitamin K epoxide reductase-like protein, 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-like protein, 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-like protein, 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

6wvb__assembly_1__model_1

6wvb__assembly_1__model_1 | I(q)

6wvb__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (2)