SAXSdb — 2dex

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

Protein-arginine deiminase type IV

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	10-mer peptide from histone H3 × 2 CALCIUM ION × 10 SULFATE ION × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PADI4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 9–671； UniProt 1–663

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	2dex
Deposition date deposition_date	2006-02-18
Structure title title	Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal peptide including Arg17
Keywords keywords	histone modification enzyme, HYDROLASE; HYDROLASE
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.

2dex__assembly_1__model_1

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

Download this curve (.dat)

2dex__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dex__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.54 Å
Rg (electron density)	37.34 Å
Total Rg	37.77 Å
Atom count	9996
Residues	1264
Excluded volume	178960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dex__assembly_1__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	Protein-arginine deiminase type IV
Molecular weight formula_weight	74933.8 kDa
EC 编号 ec_number	3.5.3.15
Mutation mutation	C645A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	5190

GPLGSPEFMAQGTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVVDIAHSPPAKKKSTGSSTWPLDPGVEVTLTMKAASGSTGDQKVQISYYGPKTPPVKALLYLTAVEISLCADITRTGKVKPTRAVKDQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATRGKLSSKCSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLTICPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIRHGEVHAGTNVRRKPFSFKWWNMVP

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	10-mer peptide from histone H3
Molecular weight formula_weight	1128.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

LAPRKQLATK

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	192

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2dexx1
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.9 — Peptidylarginine deiminase Pad4, middle domain
Family Family family	b.2.9.1 — Peptidylarginine deiminase Pad4, middle domain

Domain ID domain_id	d2dexx2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.6 — Peptidylarginine deiminase Pad4, N-terminal domain

Domain ID domain_id	d2dexx3
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.126.1.5 — Peptidylarginine deiminase Pad4, catalytic C-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id	2dexX01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1860 — Protein-arginine deiminase, N-terminal domain

Domain ID domain_id	2dexX02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1700 — Protein-arginine deiminase, central domain

Domain ID domain_id	2dexX03
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	146.072 Å
Unit-cell length b length_b	60.103 Å
Unit-cell length c length_c	115.703 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	124.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	33.130 Å
R factor r_factor	0.2070
R_work r_work	0.2025
R_free r_free	0.2470

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal peptide including Arg17

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

Protein-arginine deiminase type IV

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

2dex__assembly_1__model_1

2dex__assembly_1__model_1 | I(q)

2dex__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal peptide including Arg17

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

Protein-arginine deiminase type IV

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

2dex__assembly_1__model_1

2dex__assembly_1__model_1 | I(q)

2dex__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)