SAXSdb — 2ybs

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

LYSINE-SPECIFIC DEMETHYLASE 4A

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 H3.1T × 1 （Q16695） NICKEL (II) ION × 1 ZINC ION × 1 GLYCEROL × 1 (2S)-2-HYDROXYPENTANEDIOIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	HISTONE H3.1T × 1 （Q16695） NICKEL (II) ION × 1 ZINC ION × 1 (2S)-2-HYDROXYPENTANEDIOIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDM4A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–381； UniProt 1–359 Author chain B； PDBConstruct 23–381； UniProt 1–359

HISTONE H3.1T

OrganismNot specified

UniProt Q16695

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	LYSINE-SPECIFIC DEMETHYLASE 4A × 1 （O75164） NICKEL (II) ION × 1 ZINC ION × 1 GLYCEROL × 1 (2S)-2-HYDROXYPENTANEDIOIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	LYSINE-SPECIFIC DEMETHYLASE 4A × 1 （O75164） NICKEL (II) ION × 1 ZINC ION × 1 (2S)-2-HYDROXYPENTANEDIOIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H31T_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–12； UniProt 31–42 Author chain D； PDBConstruct 1–12； UniProt 31–42

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	2ybs
Deposition date deposition_date	2011-03-10
Structure title title	JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41)
Keywords keywords	;OXIDOREDUCTASE-PEPTIDE COMPLEX, NON-HEME IRON, DIOXYGENASE, DOUBLE-STRANDED BETA HELIX, DSBH, FACIAL TRIAD, METAL BINDING PROTEIN, EPIGENETIC AND TRANSCRIPTION REGULATION, CHROMATIN REGULATOR, HYDROXYLATION ;; OXIDOREDUCTASE/PEPTIDE
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.

2ybs__assembly_1__model_1

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

Download this curve (.dat)

2ybs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ybs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.98 Å
Rg (electron density)	19.93 Å
Total Rg	20.99 Å
Atom count	2961
Residues	359
Excluded volume	52858 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ybs__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ybs__assembly_2__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	LYSINE-SPECIFIC DEMETHYLASE 4A
Molecular weight formula_weight	44326.3 kDa
EC 编号 ec_number	1.14.11.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6395

MHHHHHHSSGVDLGTENLYFQSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL

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 H3.1T
Molecular weight formula_weight	1356.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

PATGGVKKPHRY

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	(2S)-2-HYDROXYPENTANEDIOIC ACID
Molecular weight formula_weight	148.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	475

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2ybsA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	2ybsB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

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Unit-cell length a length_a	100.924 Å
Unit-cell length b length_b	149.354 Å
Unit-cell length c length_c	57.271 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.320 Å
Low-resolution limit resolution_low	30.140 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2370

JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41)

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

LYSINE-SPECIFIC DEMETHYLASE 4A

State in the Current Structure

Other States of the Same Protein in the Database

HISTONE H3.1T

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

2ybs__assembly_1__model_1

2ybs__assembly_1__model_1 | I(q)

2ybs__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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41)

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

LYSINE-SPECIFIC DEMETHYLASE 4A

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 H3.1T

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

2ybs__assembly_1__model_1

2ybs__assembly_1__model_1 | I(q)

2ybs__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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)