3orz

PDK1 mutant bound to allosteric disulfide fragment activator 2A2

Method: X-RAY DIFFRACTION

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

3-phosphoinositide-dependent protein kinase 1

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	4-[4-(3-chlorophenyl)piperazin-1-yl]-4-oxobutane-1-thiol × 1 3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	4-[4-(3-chlorophenyl)piperazin-1-yl]-4-oxobutane-1-thiol × 1 3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	4-[4-(3-chlorophenyl)piperazin-1-yl]-4-oxobutane-1-thiol × 1 3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	4-[4-(3-chlorophenyl)piperazin-1-yl]-4-oxobutane-1-thiol × 1 3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDPK1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–316； UniProt 51–359 Author chain B； PDBConstruct 8–316； UniProt 51–359 Author chain C； PDBConstruct 8–316； UniProt 51–359 Author chain D； PDBConstruct 8–316； UniProt 51–359

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	3orz
Deposition date deposition_date	2010-09-08
Structure title title	PDK1 mutant bound to allosteric disulfide fragment activator 2A2
Keywords keywords	;C helix, Ser/Thr-kinase, AGC kinase, allostery, transferase, allosteric activator, bisindolylmaleimide, disulfide, kinase, PDK1, TRANSFERASE-TRANSFERASE ACTIVATOR complex ;; TRANSFERASE/TRANSFERASE ACTIVATOR
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.

3orz__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3orz__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3orz__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.45 Å
Rg (electron density)	19.28 Å
Total Rg	20.31 Å
Atom count	2293
Residues	278
Excluded volume	41372 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3orz__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3orz__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3orz__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3orz__assembly_4__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	3-phosphoinositide-dependent protein kinase 1
Molecular weight formula_weight	36177.5 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	T148C
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	9976

GAMDPEFMDGTAAEPRPGAGSLQHAQPPPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFCFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT

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	4-[4-(3-chlorophenyl)piperazin-1-yl]-4-oxobutane-1-thiol
Molecular weight formula_weight	298.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE
Molecular weight formula_weight	438.5 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	809

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3orza_
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	d3orzb_
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	d3orzc_
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	d3orzd_
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 (8 domains)

Domain ID domain_id	3orzA01
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	3orzA02
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	3orzB01
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	3orzB02
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	3orzC01
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	3orzC02
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	3orzD01
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	3orzD02
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	243.134 Å
Unit-cell length b length_b	116.124 Å
Unit-cell length c length_c	37.702 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	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	41.985 Å
R factor r_factor	0.2203
R_work r_work	0.2178
R_free r_free	0.2651

PDK1 mutant bound to allosteric disulfide fragment activator 2A2

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

3-phosphoinositide-dependent protein kinase 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

3orz__assembly_2__model_1

3orz__assembly_2__model_1 | I(q)

3orz__assembly_2__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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

PDK1 mutant bound to allosteric disulfide fragment activator 2A2

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

3-phosphoinositide-dependent protein kinase 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

3orz__assembly_2__model_1

3orz__assembly_2__model_1 | I(q)

3orz__assembly_2__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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)