9ho3

Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2OG, nitric oxide, and Factor X peptide fragment

Method: X-RAY DIFFRACTION

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

Aspartyl/asparaginyl beta-hydroxylase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Coagulation factor X × 1 （P00742） SODIUM ION × 1 POTASSIUM ION × 1 FE (III) ION × 1 2-OXOGLUTARIC ACID × 1 NITRIC OXIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASPH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–429； UniProt 330–758

Coagulation factor X

OrganismNot specified

UniProt P00742

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Aspartyl/asparaginyl beta-hydroxylase × 1 （Q12797） SODIUM ION × 1 POTASSIUM ION × 1 FE (III) ION × 1 2-OXOGLUTARIC ACID × 1 NITRIC OXIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FA10_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–39； UniProt 86–124

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	9ho3
Deposition date deposition_date	2024-12-11
Structure title title	Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2OG, nitric oxide, and Factor X peptide fragment
Keywords keywords	Aspartyl/Asparaginyl beta-hydroxylase, AspH, 2-oxoglutarate, nitric oxide, oxygen mimick, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

9ho3__assembly_1__model_1

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

Download this curve (.dat)

9ho3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ho3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.17 Å
Rg (electron density)	26.15 Å
Total Rg	26.84 Å
Atom count	3522
Residues	448
Excluded volume	62306 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ho3__assembly_1__model_1`	dimeric （2）	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 (8)

Entity 1 Entity 1 polymer

Description description	Aspartyl/asparaginyl beta-hydroxylase
Molecular weight formula_weight	49405.3 kDa
EC 编号 ec_number	1.14.11.16
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	3680

KPKLLNKFDKTIKAELDAAEKLRKRGKIEEAVNAFKELVRKYPQSPRARYGKAQCEDDLAEKRRSNEVLRGAIETYQEVASLPDVPADLLKLSLKRRSDRQQFLGHMRGSLLTLQRLVQLFPNDTSLKNDLGVGYLLIGDNDNAKKVYEEVLSVTPNDGFAKVHYGFILKAQNKIAESIPYLKEGIESGDPGTDDGRFYFHLGDAMQRVGNKEAYKWYELGHKRGHFASVWQRSLYNVNGLKAQPWWTPKETGYTELVKSLERNWKLIRDEGLAVMDKAKGLFLPEDENLREKGDWSQFTLWQQGRRNENACKGAPKTCTLLEKFPETTGCRRGQIKYSIMHPGTHVWPHTGPTNCRLRMHLGLVIPKEGCKIRCANETKTWEEGKVLIFDDSFEHEVWQDASSFRLIFIVDVWHPELTPQQRRSLPAI

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Coagulation factor X
Molecular weight formula_weight	4190.4 kDa
Mutation mutation	C90S, C95S, C112S, C121S
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DGDQSETSPSQNQGKCKDGLGEYTCTSLEGFEGKNSELF

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2-OXOGLUTARIC ACID
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	NITRIC OXIDE
Molecular weight formula_weight	30.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	150

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Unit-cell length a length_a	49.830 Å
Unit-cell length b length_b	86.490 Å
Unit-cell length c length_c	123.230 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.390 Å
Low-resolution limit resolution_low	46.200 Å
R factor r_factor	0.2009
R_work r_work	0.1988
R_free r_free	0.2422

Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2OG, nitric oxide, and Factor X peptide fragment

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

Aspartyl/asparaginyl beta-hydroxylase

State in the Current Structure

Other States of the Same Protein in the Database

Coagulation factor X

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

9ho3__assembly_1__model_1

9ho3__assembly_1__model_1 | I(q)

9ho3__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2OG, nitric oxide, and Factor X peptide fragment

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

Aspartyl/asparaginyl beta-hydroxylase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Coagulation factor X

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

9ho3__assembly_1__model_1

9ho3__assembly_1__model_1 | I(q)

9ho3__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)