SAXSdb — 1vpv

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

UPF0230 protein TM1468

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PHOSPHATE ION × 1 PALMITIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PHOSPHATE ION × 1 PALMITIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1468_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–300； UniProt 1–288 Author chain B； PDBConstruct 13–300； UniProt 1–288

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	1vpv
Deposition date deposition_date	2004-11-18
Structure title title	Crystal structure of a degv lipid binding protein (tm1468) from thermotoga maritima at 2.45 A resolution
Keywords keywords	;Dak1/degv-like fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, lipid binding protein ;; LIPID BINDING 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.

1vpv__assembly_1__model_1

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

Download this curve (.dat)

1vpv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vpv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.72 Å
Rg (electron density)	18.45 Å
Total Rg	19.47 Å
Atom count	2232
Residues	276
Excluded volume	40434 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vpv__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vpv__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	UPF0230 protein TM1468
Molecular weight formula_weight	34411.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4553

MGSDKIHHHHHHMKVKILVDSTADVPFSWMEKYDIDSIPLYVVWEDGRSEPDEREPEEIMNFYKRIREAGSVPKTSQPSVEDFKKRYLKYKEEDYDVVLVLTLSSKLSGTYNSAVLASKEVDIPVYVVDTLLASGAIPLPARVAREMLENGATIEEVLKKLDERMKNKDFKAIFYVSNFDYLVKGGRVSKFQGFVGNLLKIRVCLHIENGELIPYRKVRGDKKAIEALIEKLREDTPEGSKLRVIGVHADNEAGVVELLNTLRKSYEVVDEIISPMGKVITTHVGPGTVGFGIEVLERKR

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1vpva_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.119 — DAK1/DegV-like
Superfamily Superfamily superfamily	c.119.1 — DAK1/DegV-like
Family Family family	c.119.1.1 — DegV-like

Domain ID domain_id	d1vpvb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.119 — DAK1/DegV-like
Superfamily Superfamily superfamily	c.119.1 — DAK1/DegV-like
Family Family family	c.119.1.1 — DegV-like

CATH v4.4 (4 domains)

Domain ID domain_id	1vpvA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10170 —

Domain ID domain_id	1vpvA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1180 — Hypothetical Protein Tm841; Chain: A;domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1vpvB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10170 —

Domain ID domain_id	1vpvB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1180 — Hypothetical Protein Tm841; Chain: A;domain 3
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	103.256 Å
Unit-cell length b length_b	103.256 Å
Unit-cell length c length_c	115.863 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	47.160 Å
R factor r_factor	0.1835
R_work r_work	0.1799
R_free r_free	0.2519

Crystal structure of a degv lipid binding protein (tm1468) from thermotoga maritima at 2.45 A resolution

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

UPF0230 protein TM1468

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

1vpv__assembly_1__model_1

1vpv__assembly_1__model_1 | I(q)

1vpv__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a degv lipid binding protein (tm1468) from thermotoga maritima at 2.45 A resolution

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

UPF0230 protein TM1468

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

1vpv__assembly_1__model_1

1vpv__assembly_1__model_1 | I(q)

1vpv__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)