SAXSdb — 9dpz

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

Protein-arginine deiminase type-4

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	(2S)-2-amino-2-{1-[7-(4-bromophenyl)-5,6-dimethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl]piperidin-4-yl}-1-(pyrrolidin-1-yl)ethan-1-one × 1 ;[(3S,4R)-3-amino-4-hydroxypiperidin-1-yl]{2-[1-(cyclopropylmethyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-7-methoxy-1-methyl-1H-benzimidazol-5-yl}methanone ; × 1 water × 1	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 A； 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	9dpz
Deposition date deposition_date	2024-09-23
Last revision last_revision	2025-05-28
Structure title title	Potent inhibition of the protein arginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site
Keywords keywords	inhibitor, allosteric, HYDROLASE, 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.

9dpz__assembly_1__model_1

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

Download this curve (.dat)

9dpz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9dpz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.32 Å
Rg (electron density)	33.84 Å
Total Rg	34.10 Å
Atom count	4600
Residues	596
Excluded volume	82131 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9dpz__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Protein-arginine deiminase type-4
Molecular weight formula_weight	74965.9 kDa
EC 编号 ec_number	3.5.3.15
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	4627

GPLGSPEFMAQGTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVVDIAHSPPAKKKSTGSSTWPLDPGVEVTLTMKAASGSTGDQKVQISYYGPKTPPVKALLYLTAVEISLCADITRTGKVKPTRAVKDQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATRGKLSSKCSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLTICPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIRHGEVHCGTNVRRKPFSFKWWNMVP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Insect cell expression vector pTIE1

Entity 2 Entity 2 non-polymer

Description description	(2S)-2-amino-2-{1-[7-(4-bromophenyl)-5,6-dimethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl]piperidin-4-yl}-1-(pyrrolidin-1-yl)ethan-1-one
Molecular weight formula_weight	511.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	;[(3S,4R)-3-amino-4-hydroxypiperidin-1-yl]{2-[1-(cyclopropylmethyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-7-methoxy-1-methyl-1H-benzimidazol-5-yl}methanone ;
Molecular weight formula_weight	474.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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Unit-cell length a length_a	147.339 Å
Unit-cell length b length_b	60.421 Å
Unit-cell length c length_c	113.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.36 °
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	monoclinic

Resolution resolution	2.410 Å
Low-resolution limit resolution_low	47.260 Å
R factor r_factor	0.1921
R_work r_work	0.1900
R_free r_free	0.2341

Potent inhibition of the protein arginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site

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

Protein-arginine deiminase type-4

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

9dpz__assembly_1__model_1

9dpz__assembly_1__model_1 | I(q)

9dpz__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Potent inhibition of the protein arginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site

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

Protein-arginine deiminase type-4

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

9dpz__assembly_1__model_1

9dpz__assembly_1__model_1 | I(q)

9dpz__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)