8re8

Aspartyl/Asparaginyl beta-hydroxylase (AspH) R688Q variant in complex with Mn, (3R)-methyl-2-oxoglutarate and a Factor X derived 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） (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid × 1 DI(HYDROXYETHYL)ETHER × 5 MANGANESE (II) ION × 1 CHLORIDE ION × 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 1–444； UniProt 315–758

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） (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid × 1 DI(HYDROXYETHYL)ETHER × 5 MANGANESE (II) ION × 1 CHLORIDE ION × 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	8re8
Deposition date deposition_date	2023-12-10
Structure title title	Aspartyl/Asparaginyl beta-hydroxylase (AspH) R688Q variant in complex with Mn, (3R)-methyl-2-oxoglutarate and a Factor X derived peptide fragment
Keywords keywords	AspH, Aspartyl/Asparaginyl beta-hydroxylase, 2-oxoglutarate, 2OG, alpha-ketoglutarate, substrate analogues, 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.

8re8__assembly_1__model_1

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

Download this curve (.dat)

8re8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8re8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.35 Å
Rg (electron density)	26.28 Å
Total Rg	27.04 Å
Atom count	3578
Residues	447
Excluded volume	63412 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8re8__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 (7)

Entity 1 Entity 1 polymer

Description description	Aspartyl/asparaginyl beta-hydroxylase
Molecular weight formula_weight	51164.4 kDa
EC 编号 ec_number	1.14.11.16
Mutation mutation	R688Q
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	3938

RKTDDPEQKAKVKKKKPKLLNKFDKTIKAELDAAEKLRKRGKIEEAVNAFKELVRKYPQSPRARYGKAQCEDDLAEKRRSNEVLRGAIETYQEVASLPDVPADLLKLSLKRRSDRQQFLGHMRGSLLTLQRLVQLFPNDTSLKNDLGVGYLLIGDNDNAKKVYEEVLSVTPNDGFAKVHYGFILKAQNKIAESIPYLKEGIESGDPGTDDGRFYFHLGDAMQRVGNKEAYKWYELGHKRGHFASVWQRSLYNVNGLKAQPWWTPKETGYTELVKSLERNWKLIRDEGLAVMDKAKGLFLPEDENLREKGDWSQFTLWQQGRRNENACKGAPKTCTLLEKFPETTGCRRGQIKYSIMHPGTHVWPHTGPTNCRLQMHLGLVIPKEGCKIRCANETKTWEEGKVLIFDDSFEHEVWQDASSFRLIFIVDVWHPELTPQQRRSLPAI

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	(3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid
Molecular weight formula_weight	160.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	314

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Unit-cell length a length_a	50.604 Å
Unit-cell length b length_b	85.998 Å
Unit-cell length c length_c	123.963 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	1.850 Å
Low-resolution limit resolution_low	46.850 Å
R factor r_factor	0.1788
R_work r_work	0.1775
R_free r_free	0.2082

Aspartyl/Asparaginyl beta-hydroxylase (AspH) R688Q variant in complex with Mn, (3R)-methyl-2-oxoglutarate and a Factor X derived 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

8re8__assembly_1__model_1

8re8__assembly_1__model_1 | I(q)

8re8__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 (7)

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 water

7. Citations (1)

Aspartyl/Asparaginyl beta-hydroxylase (AspH) R688Q variant in complex with Mn, (3R)-methyl-2-oxoglutarate and a Factor X derived 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

8re8__assembly_1__model_1

8re8__assembly_1__model_1 | I(q)

8re8__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 (7)

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 water

7. Citations (1)