2qr1

Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with ADP

Method: X-RAY DIFFRACTION

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

SNF1-like protein kinase ssp2

Schizosaccharomyces pombe

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	SPCC1919.03c protein × 1 （P78789） Protein C1556.08c × 1 （Q10343） ADENOSINE-5'-DIPHOSPHATE × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	SPCC1919.03c protein × 1 （P78789） Protein C1556.08c × 1 （Q10343） ADENOSINE-5'-DIPHOSPHATE × 2 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	SPCC1919.03c protein × 2 （P78789） Protein C1556.08c × 2 （Q10343） ADENOSINE-5'-DIPHOSPHATE × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNF1_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–137； UniProt 440–576 Author chain C； PDBConstruct 1–137； UniProt 440–576

SPCC1919.03c protein

Schizosaccharomyces pombe

UniProt P78789

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	SNF1-like protein kinase ssp2 × 1 （O74536） Protein C1556.08c × 1 （Q10343） ADENOSINE-5'-DIPHOSPHATE × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	SNF1-like protein kinase ssp2 × 1 （O74536） Protein C1556.08c × 1 （Q10343） ADENOSINE-5'-DIPHOSPHATE × 2 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	SNF1-like protein kinase ssp2 × 2 （O74536） Protein C1556.08c × 2 （Q10343） ADENOSINE-5'-DIPHOSPHATE × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P78789_SCHPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–97； UniProt 203–298 Author chain D； PDBConstruct 2–97； UniProt 203–298

Protein C1556.08c

Schizosaccharomyces pombe

UniProt Q10343

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	SNF1-like protein kinase ssp2 × 1 （O74536） SPCC1919.03c protein × 1 （P78789） ADENOSINE-5'-DIPHOSPHATE × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	SNF1-like protein kinase ssp2 × 1 （O74536） SPCC1919.03c protein × 1 （P78789） ADENOSINE-5'-DIPHOSPHATE × 2 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	SNF1-like protein kinase ssp2 × 2 （O74536） SPCC1919.03c protein × 2 （P78789） ADENOSINE-5'-DIPHOSPHATE × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YL28_SCHPO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 3–334； UniProt 3–334 Author chain G； PDBConstruct 3–334； UniProt 3–334

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	2qr1
Deposition date deposition_date	2007-07-27
Structure title title	Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with ADP
Keywords keywords	AMPK, ADP, ATP-binding, Kinase, Nucleotide-binding, Serine/threonine-protein kinase, Transferase, CBS domain; 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.

2qr1__assembly_1__model_1

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

Download this curve (.dat)

2qr1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qr1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.34 Å
Rg (electron density)	26.81 Å
Total Rg	27.52 Å
Atom count	4247
Residues	531
Excluded volume	76179 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qr1__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qr1__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2qr1__assembly_3__model_1`	hexameric （6）	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	SNF1-like protein kinase ssp2
Molecular weight formula_weight	15903.4 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8544

SQSTRKKSRRNKWHFGVRCRGDAPEILLAVYRALQRAGAQFTVPKPVNGKYRSDMYTIKSRWEIPHCKREGKNTYAYIELQLYEVMPGCFMLDVKSNGYKDIYSHPERTADHGMDDLKSSFPFLDLCAMLVCKLFSA

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	SPCC1919.03c protein
Molecular weight formula_weight	10865.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSESEQYSTEIPAFLTSNTLQELKLPKPPSLPPHLEKCILNSNTAYKEDQSVLPNPNHVLLNHLAAANTQLGVLALSATTRYHRKYVTTAMFKNFDV

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Protein C1556.08c
Molecular weight formula_weight	37436.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,E

AMDVQETQKGALKEIQAFIRSRTSYDVLPTSFRLIVFDVTLFVKTSLSLLTLNNIVSAPLWDSEANKFAGLLTMADFVNVIKYYYQSSSFPEAIAEIDKFRLLGLREVERKIGAIPPETIYVHPMHSLMDACLAMSKSRARRIPLIDVDGETGSEMIVSVLTQYRILKFISMNCKETAMLRVPLNQMTIGTWSNLATASMETKVYDVIKMLAEKNISAVPIVNSEGTLLNVYESVDVMHLIQDGDYSNLDLSVGEALLKRPANFDGVHTCRATDRLDGIFDAIKHSRVHRLFVVDENLKLEGILSLADILNYIIYDKTTTPGVPEQTDNFESAV

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	79

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2qr1a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.6 — KA1-like
Family Family family	d.129.6.2 — Ssp2 C-terminal domain-like

Domain ID domain_id	d2qr1b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.353 — AMPKBI-like
Superfamily Superfamily superfamily	d.353.1 — AMPKBI-like
Family Family family	d.353.1.1 — AMPKBI-like

Domain ID domain_id	d2qr1c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.6 — KA1-like
Family Family family	d.129.6.2 — Ssp2 C-terminal domain-like

Domain ID domain_id	d2qr1d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.353 — AMPKBI-like
Superfamily Superfamily superfamily	d.353.1 — AMPKBI-like
Family Family family	d.353.1.1 — AMPKBI-like

Domain ID domain_id	d2qr1e1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2qr1e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2qr1g1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2qr1g2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d2qr1g3
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 (8 domains)

Domain ID domain_id	2qr1A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	80 — Kinase associated domain 1, KA1

Domain ID domain_id	2qr1B01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	290 —

Domain ID domain_id	2qr1C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	80 — Kinase associated domain 1, KA1

Domain ID domain_id	2qr1D01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	290 —

Domain ID domain_id	2qr1E01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

Domain ID domain_id	2qr1E02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

Domain ID domain_id	2qr1G01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

Domain ID domain_id	2qr1G02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

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Unit-cell length a length_a	168.293 Å
Unit-cell length b length_b	78.087 Å
Unit-cell length c length_c	108.553 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	124.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	48.280 Å
R factor r_factor	0.2106
R_work r_work	0.2064
R_free r_free	0.2894

Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with ADP

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

SNF1-like protein kinase ssp2

State in the Current Structure

Other States of the Same Protein in the Database

SPCC1919.03c protein

State in the Current Structure

Other States of the Same Protein in the Database

Protein C1556.08c

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

2qr1__assembly_1__model_1

2qr1__assembly_1__model_1 | I(q)

2qr1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with ADP

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

SNF1-like protein kinase ssp2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SPCC1919.03c protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein C1556.08c

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

2qr1__assembly_1__model_1

2qr1__assembly_1__model_1 | I(q)

2qr1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)