SAXSdb — 3p8p

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

N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	N~5~-[(1E)-pentanimidoyl]-L-ornithine × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N~5~-[(1E)-pentanimidoyl]-L-ornithine × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDAH1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–308； UniProt 1–285 Author chain B； PDBConstruct 24–308； UniProt 1–285

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	3p8p
Deposition date deposition_date	2010-10-14
Structure title title	Crystal Structure of Human Dimethylarginine Dimethylaminohydrolase-1 (DDAH-1) variant C274S bound with N5-(1-iminopentyl)-L-ornithine
Keywords keywords	DDAH, NITRIC OXIDE SYNTHASE REGULATOR, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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.

3p8p__assembly_1__model_1

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

Download this curve (.dat)

3p8p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3p8p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.40 Å
Rg (electron density)	17.13 Å
Total Rg	18.10 Å
Atom count	2071
Residues	275
Excluded volume	36927 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3p8p__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3p8p__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 (3)

Entity 1 Entity 1 polymer

Description description	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Molecular weight formula_weight	33607.4 kDa
EC 编号 ec_number	3.5.3.18
Mutation mutation	C274S
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	4247

MGSSHHHHHHSSGLVPRGSHMASMAGLGHPAAFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTSCSVLINKKVDS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N~5~-[(1E)-pentanimidoyl]-L-ornithine
Molecular weight formula_weight	215.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	130

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3p8pa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.0 — automated matches

Domain ID domain_id	d3p8pb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3p8pA00
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

Domain ID domain_id	3p8pB00
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

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Unit-cell length a length_a	47.226 Å
Unit-cell length b length_b	79.632 Å
Unit-cell length c length_c	73.608 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2275
R_free r_free	0.3050

Crystal Structure of Human Dimethylarginine Dimethylaminohydrolase-1 (DDAH-1) variant C274S bound with N5-(1-iminopentyl)-L-ornithine

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

N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

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

3p8p__assembly_1__model_1

3p8p__assembly_1__model_1 | I(q)

3p8p__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Human Dimethylarginine Dimethylaminohydrolase-1 (DDAH-1) variant C274S bound with N5-(1-iminopentyl)-L-ornithine

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

N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

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

3p8p__assembly_1__model_1

3p8p__assembly_1__model_1 | I(q)

3p8p__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)