SAXSdb — 7r6y

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

Pyruvate kinase PKM

Oryctolagus cuniculus

UniProt P11974

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ACETATE ION × 9 OXALATE ION × 4 MAGNESIUM ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KPYM_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–531； UniProt 1–531 Author chain B； PDBConstruct 1–531； UniProt 1–531 Author chain C； PDBConstruct 1–531； UniProt 1–531 Author chain D； PDBConstruct 1–531； UniProt 1–531

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	7r6y
Deposition date deposition_date	2021-06-24
Structure title title	E117K mutant pyruvate kinase from rabbit muscle
Keywords keywords	Mutant, Magnesium, oxalate, pyruvate kinase, PK, 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.

7r6y__assembly_1__model_1

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

Download this curve (.dat)

7r6y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7r6y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.84 Å
Rg (electron density)	38.46 Å
Total Rg	38.76 Å
Atom count	14352
Residues	1897
Excluded volume	255700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7r6y__assembly_1__model_1`	tetrameric （4）	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	Pyruvate kinase PKM
Molecular weight formula_weight	58130.1 kDa
EC 编号 ec_number	2.7.1.40
Mutation mutation	E117K
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	15009

MSKSHSEAGSAFIQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVETLKEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPKIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVDVGSKVYVDDGLISLQVKQKGPDFLVTEVENGGFLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKILGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMIIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAMFHRKLFEELARSSSHSTDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQEAWAEDVDLRVNLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	Rabbit
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	OXALATE ION
Molecular weight formula_weight	88.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	638

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7r6yA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily	10 — PK beta-barrel domain-like

Domain ID domain_id	7r6yA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	7r6yB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily	10 — PK beta-barrel domain-like

Domain ID domain_id	7r6yB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — Pyruvate kinase, C-terminal domain

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Unit-cell length a length_a	108.340 Å
Unit-cell length b length_b	121.830 Å
Unit-cell length c length_c	161.370 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	44.970 Å
R factor r_factor	0.2033
R_work r_work	0.2009
R_free r_free	0.2496

E117K mutant pyruvate kinase from rabbit muscle

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

Pyruvate kinase PKM

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

7r6y__assembly_1__model_1

7r6y__assembly_1__model_1 | I(q)

7r6y__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

E117K mutant pyruvate kinase from rabbit muscle

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

Pyruvate kinase PKM

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

7r6y__assembly_1__model_1

7r6y__assembly_1__model_1 | I(q)

7r6y__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)