SAXSdb — 6evl

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

Prolyl 4-hydroxylase subunit alpha-2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 163–257	Not recorded	SO4 SULFATE ION × 1 DMS DIMETHYL SULFOXIDE × 1 GLY GLYCINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；2.45 M ammonium sulphate, 10% DMSO, 100 mM MOPS, pH 6.5	Resolution 1.87 Å R-free 0.224

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6EVL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6EVM Crystal structure of a Pro-9 complexed peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase Deposited 2017-11-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 163–257（95 aa）	Not recorded	SO4 SULFATE ION × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；2.45 M ammonium sulphate, 10% DMSO, 2.5 mM Pro-9, 4% hexenediol, 100 mM MOPS	Resolution 2.00 Å R-free 0.219
6EVN Crystal structure of peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase complex with Pro-Pro-Gly-Pro-Ala-Gly-Pro-Pro-Gly. Deposited 2017-11-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 163–257（95 aa）	Not recorded	SO4 SULFATE ION × 2 DMS DIMETHYL SULFOXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；2.45 M ammonium sulphate, 10% DMSO, 5 mM PPGPAGPPG, 5% D-galactose, 100 mM MOPS, pH 6.5	Resolution 1.48 Å R-free 0.179
6EVO Crystal structure the peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Arg-Gly-Pro-Pro-Gly. Deposited 2017-11-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 163–257（95 aa）	Not recorded	SO4 SULFATE ION × 2 DMS DIMETHYL SULFOXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；2.45 M ammonium sulphate, 10% DMSO, 5 mM PPGPRGPPG, 10 mM EDTA, 100 mM MOPS	Resolution 1.55 Å R-free 0.180
6EVP Crystal structure the peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Glu-Gly-Pro-Pro-Gly. Deposited 2017-11-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 163–257（95 aa）	Not recorded	SO4 SULFATE ION × 1 DMS DIMETHYL SULFOXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；2.45 M ammonium sulphate, 10% DMSO, 100 mM MOPS, 5 mM PPGPEGPPG, 5% PEG 400, 100 mM MOPS.	Resolution 1.68 Å R-free 0.215
7ZSC Crystal structure of the heterodimeric human C-P4H-II with truncated alpha subunit (C-P4H-II delta281) Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 282–535（254 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；278 K；20% (w/v) PEG4000, 0.2 M lithium sulfate, 0.1 M MES, 3% methanol	Resolution 3.85 Å R-free 0.278
7ZSC Crystal structure of the heterodimeric human C-P4H-II with truncated alpha subunit (C-P4H-II delta281) Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 282–535（254 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；278 K；20% (w/v) PEG4000, 0.2 M lithium sulfate, 0.1 M MES, 3% methanol	Resolution 3.85 Å R-free 0.278
9HTD Peptide-substrate-binding (PSB) domain of human type II collagen prolyl 4-hydroxylase complexed with Pro-Hyp-Gly-Pro-Ala-Gly-Pro-Hyp-Gly. Deposited 2024-12-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 163–257（95 aa）	Not recorded	GLY GLYCINE × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；278 K；2M ammonium sulphate, 10% dioxane, 100 mM MES, 2 mM Pro-Hyp-Gly-Pro-Ala-Gly-Pro-Hyp-Gly.	Resolution 1.75 Å R-free 0.195

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	P4HA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–102； UniProt 163–257

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	6evl
Deposition date deposition_date	2017-11-02
Structure title title	Crystal structure of an unlignaded peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase
Keywords keywords	tetratricopeptide repeat, collagen synthesis, prolyl 4-hydroxylase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.50 Å
Radius of gyration Rg (electron density) rg_electron	13.27 Å
Forward intensity I(0) i0	2758680.00
Molecular weight molecular_weight	11119.0 kDa
Excluded volume excluded_volume	13691 Å³
Envelope volume envelope_volume	15368 Å³
Hydration-shell volume shell_volume	10203 Å³
Envelope diameter envelope_diameter	51.6 Å
Shell Rg shell_rg	18.66 Å
Envelope Rg envelope_rg	13.76 Å
Shape Rg shape_rg	13.25 Å
Total Rg total_rg	14.49 Å
Total atoms total_atoms	779
Residues n_residues	94
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	51.0 Å
Rg (real space) rg_real	14.47 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	2.7590e+06
I(0) uncertainty (real space) i0_real_error	3.1620e+04
Rg (reciprocal space) rg_reciprocal	14.48 Å
I(0) (reciprocal space) i0_reciprocal	2759000.0000
Solution quality estimate total_estimate	0.7033
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.3 Å
Skewness Skewness skewness	0.335
Kurtosis Kurtosis kurtosis	-0.129
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	750000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.699; Stabil: 0.999; Sysdev: 0.368; Positv: 1.000; Valcen: 0.943; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Prolyl 4-hydroxylase subunit alpha-2
Molecular weight formula_weight	11920.3 kDa
EC 编号 ec_number	1.14.11.2
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	939

MHHHHHHMLSVDDCFGMGRSAYNEGDYYHTVLWMEQVLKQLDAGEEATTTKSQVLDYLSYAVFQLGDLHRALELTRRLLSLDPSHERAGGNLRYFEQLLEEE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCINE
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	122

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6evla_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.8 — TPR-like
Family Family family	a.118.8.1 — Tetratricopeptide repeat (TPR)

CATH v4.4 (1 domains)

Domain ID domain_id	6evlA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

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8. Citations (1)

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Unit-cell length a length_a	55.449 Å
Unit-cell length b length_b	55.449 Å
Unit-cell length c length_c	71.705 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.870 Å
Low-resolution limit resolution_low	48.000 Å
R factor r_factor	0.1861
R_work r_work	0.1818
R_free r_free	0.2243

fit	/app/data/saxs_computation/ev/6evl/6evl.fit
pddf	/app/data/pr_computation/ev/6evl/6evl.pr.out
profile	/app/data/saxs_computation/ev/6evl/6evl.dat

Crystal structure of an unlignaded peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase

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

Prolyl 4-hydroxylase subunit alpha-2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction