3dls

Crystal structure of human PAS kinase bound to ADP

Method: X-RAY DIFFRACTION

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

PAS domain-containing serine/threonine-protein kinase

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	MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 3 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 3	MAGNESIUM ION × 12 ADENOSINE-5'-DIPHOSPHATE × 3 water × 3	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 3	MAGNESIUM ION × 7 ADENOSINE-5'-DIPHOSPHATE × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PASK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–327； UniProt 977–1300 Author chain B； PDBConstruct 4–327； UniProt 977–1300 Author chain C； PDBConstruct 4–327； UniProt 977–1300 Author chain D； PDBConstruct 4–327； UniProt 977–1300 Author chain E； PDBConstruct 4–327； UniProt 977–1300 Author chain F； PDBConstruct 4–327； UniProt 977–1300

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	3dls
Deposition date deposition_date	2008-06-29
Structure title title	Crystal structure of human PAS kinase bound to ADP
Keywords keywords	;PAS KINASE, PASK, PROTEIN KINASE, DRUG DISCOVERY, ATP-binding, Kinase, Nucleotide-binding, Phosphoprotein, Serine/threonine-protein kinase, Transferase, Structural Genomics, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC ;; TRANSFERASE
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.

3dls__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dls__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dls__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	20.54 Å
Rg (electron density)	19.44 Å
Total Rg	20.35 Å
Atom count	2250
Residues	284
Excluded volume	40520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dls__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dls__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3dls__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3dls__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3dls__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3dls__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3dls__assembly_7__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3dls__assembly_8__model_1`	trimeric （3）	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	PAS domain-containing serine/threonine-protein kinase
Molecular weight formula_weight	37875.3 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	13724

MALEEPPKAVELEGLAACEGEYSQKYSTMSPLGSGAFGFVWTAVDKEKNKEVVVKFIKKEKVLEDCWIEDPKLGKVTLEIAILSRVEHANIIKVLDIFENQGFFQLVMEKHGSGLDLFAFIDRHPRLDEPLASYIFRQLVSAVGYLRLKDIIHRDIKDENIVIAEDFTIKLIDFGSAAYLERGKLFYTFCGTIEYCAPEVLMGNPYRGPELEMWSLGVTLYTLVFEENPFCELEETVEAAIHPPYLVSKELMSLVSGLLQPVPERRTTLEKLVTDPWVTQPVNLADYTWEEVFRVNKPESGVLSAASLEMGNRSLSDVAQAQELCGGEGHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	BACULOVIRUS

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	280

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3dlsa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3dlsb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3dlsc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3dlsd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3dlse_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3dlsf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	3dlsA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3dlsA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3dlsB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3dlsB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3dlsC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3dlsC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3dlsD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3dlsD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3dlsE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3dlsE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3dlsF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3dlsF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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Unit-cell length a length_a	85.778 Å
Unit-cell length b length_b	85.840 Å
Unit-cell length c length_c	94.154 Å
Unit-cell angle α angle_alpha	77.28 °
Unit-cell angle β angle_beta	77.50 °
Unit-cell angle γ angle_gamma	60.09 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.2440
R_work r_work	0.2410
R_free r_free	0.2970

Crystal structure of human PAS kinase bound to ADP

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

PAS domain-containing serine/threonine-protein kinase

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

3dls__assembly_4__model_1

3dls__assembly_4__model_1 | I(q)

3dls__assembly_4__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

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of human PAS kinase bound to ADP

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

PAS domain-containing serine/threonine-protein kinase

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

3dls__assembly_4__model_1

3dls__assembly_4__model_1 | I(q)

3dls__assembly_4__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

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)