SAXSdb — 1vdf

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

CARTILAGE OLIGOMERIC MATRIX PROTEIN

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	CHLORIDE ION × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COMP_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–46； UniProt 28–72 Author chain B； PDBConstruct 2–46； UniProt 28–72 Author chain C； PDBConstruct 2–46； UniProt 28–72 Author chain D； PDBConstruct 2–46； UniProt 28–72 Author chain E； PDBConstruct 2–46； UniProt 28–72

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	1vdf
Deposition date deposition_date	1996-09-12
Structure title title	ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN
Keywords keywords	EXTRACELLULAR MATRIX PROTEIN, ASSEMBLY DOMAIN, CARTILAGE, OLIGOMERIC MATRIX PROTEIN, GLYCOPROTEIN; EXTRACELLULAR MATRIX 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.

1vdf__assembly_1__model_1

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

Download this curve (.dat)

1vdf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vdf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.03 Å
Rg (electron density)	21.17 Å
Total Rg	22.29 Å
Atom count	1831
Residues	230
Excluded volume	32687 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vdf__assembly_1__model_1`	pentameric （5）	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	CARTILAGE OLIGOMERIC MATRIX PROTEIN
Molecular weight formula_weight	5299.1 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	2000

MDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG

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(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	169

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1vdfa_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.7 — Assembly domain of cartilage oligomeric matrix protein
Family Family family	h.1.7.1 — Assembly domain of cartilage oligomeric matrix protein

Domain ID domain_id	d1vdfb_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.7 — Assembly domain of cartilage oligomeric matrix protein
Family Family family	h.1.7.1 — Assembly domain of cartilage oligomeric matrix protein

Domain ID domain_id	d1vdfc_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.7 — Assembly domain of cartilage oligomeric matrix protein
Family Family family	h.1.7.1 — Assembly domain of cartilage oligomeric matrix protein

Domain ID domain_id	d1vdfd_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.7 — Assembly domain of cartilage oligomeric matrix protein
Family Family family	h.1.7.1 — Assembly domain of cartilage oligomeric matrix protein

Domain ID domain_id	d1vdfe_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.7 — Assembly domain of cartilage oligomeric matrix protein
Family Family family	h.1.7.1 — Assembly domain of cartilage oligomeric matrix protein

CATH v4.4 (5 domains)

Domain ID domain_id	1vdfA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1vdfB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1vdfC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1vdfD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1vdfE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	38.470 Å
Unit-cell length b length_b	49.470 Å
Unit-cell length c length_c	54.980 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.84 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	10

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1760
R_free r_free	—

ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN

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

CARTILAGE OLIGOMERIC MATRIX 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

1vdf__assembly_1__model_1

1vdf__assembly_1__model_1 | I(q)

1vdf__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) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (2)

ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN

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

CARTILAGE OLIGOMERIC MATRIX 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

1vdf__assembly_1__model_1

1vdf__assembly_1__model_1 | I(q)

1vdf__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) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (2)