SAXSdb — 1z9o

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

Oxysterol binding protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Vesicle-associated membrane protein-associated protein A × 6 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8K4M9_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–10； UniProt 472–481 Author chain H； PDBConstruct 1–10； UniProt 472–481 Author chain I； PDBConstruct 1–10； UniProt 472–481 Author chain J； PDBConstruct 1–10； UniProt 472–481 Author chain K； PDBConstruct 1–10； UniProt 472–481 Author chain L； PDBConstruct 1–10； UniProt 472–481

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	1z9o
Deposition date deposition_date	2005-04-03
Structure title title	1.9 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain in Complex with the Rat ORP1 FFAT Motif
Keywords keywords	;VAP-33, VAP-A, VAP-B, VAP-C, VAPA, VAPB, VAPC, VAP-33a, Scs2, ERG30, FFAT motif, ER, endoplasmic reticulum, targeting, immunoglobulin-like beta sheet, MSP homology domain, OSBP, ORP, oxysterol binding protein, PROTEIN BINDING-LIPID BINDING PROTEIN COMPLEX ;; PROTEIN BINDING/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.

1z9o__assembly_1__model_1

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

Download this curve (.dat)

1z9o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1z9o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.43 Å
Rg (electron density)	32.03 Å
Total Rg	32.49 Å
Atom count	6144
Residues	768
Excluded volume	110380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1z9o__assembly_1__model_1`	dodecameric （12）	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	Vesicle-associated membrane protein-associated protein A
Molecular weight formula_weight	14545.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	6365

GSHMAKHEQILVLDPPSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRCVFEM

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Oxysterol binding protein
Molecular weight formula_weight	1175.2 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

SEDEFYDALS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	1z9oA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1z9oB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1z9oC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1z9oD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1z9oE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1z9oF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	50.048 Å
Unit-cell length b length_b	50.033 Å
Unit-cell length c length_c	90.287 Å
Unit-cell angle α angle_alpha	90.01 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	60.03 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	14.650 Å
R factor r_factor	0.2194
R_work r_work	0.2147
R_free r_free	0.2605

1.9 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain in Complex with the Rat ORP1 FFAT Motif

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

Oxysterol binding 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

1z9o__assembly_1__model_1

1z9o__assembly_1__model_1 | I(q)

1z9o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

1.9 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain in Complex with the Rat ORP1 FFAT Motif

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

Oxysterol binding 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

1z9o__assembly_1__model_1

1z9o__assembly_1__model_1 | I(q)

1z9o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)