5fzk

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment N,3-dimethyl-N-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (N10051a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

Method: X-RAY DIFFRACTION

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

LYSINE-SPECIFIC DEMETHYLASE 5B

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	ZINC ION × 1 CHLORIDE ION × 1 MANGANESE (II) ION × 1 1,2-ETHANEDIOL × 9 N,3-dimethyl-N-[(pyridin-3-yl)methyl]-1,2-oxazole-5-carboxamide × 1 PHOSPHATE ION × 1 DIMETHYL SULFOXIDE × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDM5B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–78； UniProt 26–101 Author chain A； PDBConstruct 83–479； UniProt 374–770

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	5fzk
Deposition date deposition_date	2016-03-14
Structure title title	Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment N,3-dimethyl-N-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (N10051a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)
Keywords keywords	OXIDOREDUCTASE, JARID1B, PLU1, FRAGMENT SCREENING, STRUCTURAL GENOMICS CONSORTIUM, SGC, DIAMOND I04-1, PANDDA; OXIDOREDUCTASE
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.

5fzk__assembly_1__model_1

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

Download this curve (.dat)

5fzk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5fzk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.72 Å
Rg (electron density)	23.94 Å
Total Rg	24.90 Å
Atom count	3726
Residues	453
Excluded volume	66667 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5fzk__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 (9)

Entity 1 Entity 1 polymer

Description description	LYSINE-SPECIFIC DEMETHYLASE 5B
Molecular weight formula_weight	55214.3 kDa
EC 编号 ec_number	1.14.11.-
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	4043

SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	SPODOPTERA FRUGIPERDA

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 6 Entity 6 non-polymer

Description description	N,3-dimethyl-N-[(pyridin-3-yl)methyl]-1,2-oxazole-5-carboxamide
Molecular weight formula_weight	231.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	232

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5fzka1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.14 — Jumonji domain / Histone demethylase core

Domain ID domain_id	d5fzka2
Class class	g — Small proteins
Fold Fold fold	g.102 — Jumonji C-terminal domain-like
Superfamily Superfamily superfamily	g.102.1 — Jumonji C-terminal domain-like
Family Family family	g.102.1.0 — automated matches

Domain ID domain_id	d5fzka3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	5fzkA01
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	142.050 Å
Unit-cell length b length_b	142.050 Å
Unit-cell length c length_c	152.130 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	71.025 Å
R factor r_factor	0.2054
R_work r_work	0.2037
R_free r_free	0.2382

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment N,3-dimethyl-N-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (N10051a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

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

LYSINE-SPECIFIC DEMETHYLASE 5B

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

5fzk__assembly_1__model_1

5fzk__assembly_1__model_1 | I(q)

5fzk__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 (9)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment N,3-dimethyl-N-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (N10051a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

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

LYSINE-SPECIFIC DEMETHYLASE 5B

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

5fzk__assembly_1__model_1

5fzk__assembly_1__model_1 | I(q)

5fzk__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 (9)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

7. Citations (1)