SAXSdb — 4qyl

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

Peregrin

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	Histone H2A type 1 × 1 （P0C0S8） SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Histone H2A type 1 × 1 （P0C0S8） SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Histone H2A type 1 × 1 （P0C0S8） SULFATE ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Histone H2A type 1 × 1 （P0C0S8） SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRPF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–117； UniProt 629–742 Author chain B； PDBConstruct 4–117； UniProt 629–742 Author chain C； PDBConstruct 4–117； UniProt 629–742 Author chain D； PDBConstruct 4–117； UniProt 629–742

Histone H2A type 1

OrganismNot specified

UniProt P0C0S8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peregrin × 1 （P55201） SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Peregrin × 1 （P55201） SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Peregrin × 1 （P55201） SULFATE ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Peregrin × 1 （P55201） SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–12； UniProt 2–13 Author chain F； PDBConstruct 1–12； UniProt 2–13 Author chain G； PDBConstruct 1–12； UniProt 2–13 Author chain H； PDBConstruct 1–12； UniProt 2–13

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	4qyl
Deposition date deposition_date	2014-07-24
Structure title title	Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide
Keywords keywords	;bromodomain-PHD finger protein 1 (BRPF1), histone acetyltransferase (HAT), monocytic leukemia zinc-finger (MOZ), epigenetics, chromatin reader, bromodomain, histone post-transcriptional modification (PTM) reader domain, acetyllysine, nucleus, Protein binding ;; PROTEIN BINDING
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.

4qyl__assembly_1__model_1

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

Download this curve (.dat)

4qyl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4qyl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.30 Å
Rg (electron density)	15.29 Å
Total Rg	16.39 Å
Atom count	1028
Residues	126
Excluded volume	18288 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4qyl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4qyl__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4qyl__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4qyl__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	Peregrin
Molecular weight formula_weight	13720.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4989

GPLQLTPFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKMGID

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

Entity 2 Entity 2 polymer

Description description	Histone H2A type 1
Molecular weight formula_weight	1217.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

SGRGKQGGKARA

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	722

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4qylA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	4qylB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	4qylC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	4qylD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

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Unit-cell length a length_a	60.908 Å
Unit-cell length b length_b	55.581 Å
Unit-cell length c length_c	82.135 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	41.020 Å
R factor r_factor	0.2063
R_work r_work	0.2039
R_free r_free	0.2526

Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide

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

Peregrin

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2A type 1

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

4qyl__assembly_1__model_1

4qyl__assembly_1__model_1 | I(q)

4qyl__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide

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

Peregrin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2A type 1

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

4qyl__assembly_1__model_1

4qyl__assembly_1__model_1 | I(q)

4qyl__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)