SAXSdb — 5lvp

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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 heterocomplex	Heteromer	Protein 2	hydrophobic-motif peptide of PKB/Akt × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	hydrophobic-motif peptide of PKB/Akt × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	hydrophobic-motif peptide of PKB/Akt × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	hydrophobic-motif peptide of PKB/Akt × 1 ADENOSINE-5'-TRIPHOSPHATE × 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 2–311； UniProt 50–359 Author chain B； PDBConstruct 2–311； UniProt 50–359 Author chain C； PDBConstruct 2–311； UniProt 50–359 Author chain D； PDBConstruct 2–311； UniProt 50–359

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	5lvp
Deposition date deposition_date	2016-09-14
Structure title title	Human PDK1 Kinase Domain in Complex with an HM-Peptide Bound to the PIF-Pocket
Keywords keywords	protein kinase, allosteric regulation, small compounds, PIF-pocket, Transferase; 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.

5lvp__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5lvp__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5lvp__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	20.42 Å
Rg (electron density)	19.40 Å
Total Rg	20.51 Å
Atom count	2301
Residues	280
Excluded volume	41426 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5lvp__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5lvp__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5lvp__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5lvp__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 (5)

Entity 1 Entity 1 polymer

Description description	3-phosphoinositide-dependent protein kinase 1
Molecular weight formula_weight	35392.6 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	Y288G, Q292A
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	9538

GAMDGTAAEPRPGAGSLQHAQPPPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT

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 polymer

Description description	hydrophobic-motif peptide of PKB/Akt
Molecular weight formula_weight	1511.5 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

KGAGGGGFPQFSYSA

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	286

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5lvpA01
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	5lvpA02
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	5lvpB01
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	5lvpB02
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	5lvpC01
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	5lvpC02
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	5lvpD01
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	5lvpD02
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	47.830 Å
Unit-cell length b length_b	168.510 Å
Unit-cell length c length_c	94.880 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.06 °
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	2.500 Å
Low-resolution limit resolution_low	94.745 Å
R factor r_factor	0.1764
R_work r_work	0.1737
R_free r_free	0.2257

Human PDK1 Kinase Domain in Complex with an HM-Peptide Bound to the PIF-Pocket

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

5lvp__assembly_3__model_1

5lvp__assembly_3__model_1 | I(q)

5lvp__assembly_3__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Human PDK1 Kinase Domain in Complex with an HM-Peptide Bound to the PIF-Pocket

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

5lvp__assembly_3__model_1

5lvp__assembly_3__model_1 | I(q)

5lvp__assembly_3__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)