8f6m

Complex of Rabbit muscle pyruvate kinase with ADP and the phosphonate analogue of PEP mimicking the Michaelis complex.

Method: X-RAY DIFFRACTION

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

Pyruvate kinase PKM

OrganismNot specified

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	ADENOSINE-5'-DIPHOSPHATE × 2 SUCCINIC ACID × 5 MANGANESE (II) ION × 7 POTASSIUM ION × 4 ALANINE × 4 GLYCEROL × 13 (E)-2-METHYL-3-PHOSPHONOACRYLATE × 3 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	ADENOSINE-5'-DIPHOSPHATE × 3 SUCCINIC ACID × 7 MANGANESE (II) ION × 8 POTASSIUM ION × 4 ALANINE × 4 GLYCEROL × 13 (E)-2-METHYL-3-PHOSPHONOACRYLATE × 1 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 Author chain E； PDBConstruct 1–531； UniProt 1–531 Author chain F； PDBConstruct 1–531； UniProt 1–531 Author chain G； PDBConstruct 1–531； UniProt 1–531 Author chain H； 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	8f6m
Deposition date deposition_date	2022-11-16
Structure title title	Complex of Rabbit muscle pyruvate kinase with ADP and the phosphonate analogue of PEP mimicking the Michaelis complex.
Keywords keywords	glycolysis, metabolic kinase, central metabolism, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
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.

8f6m__assembly_1__model_1

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

Download this curve (.dat)

8f6m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8f6m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.55 Å
Rg (electron density)	40.45 Å
Total Rg	40.73 Å
Atom count	16080
Residues	2062
Excluded volume	287270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8f6m__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8f6m__assembly_2__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 (9)

Entity 1 Entity 1 polymer

Description description	Pyruvate kinase PKM
Molecular weight formula_weight	58114.0 kDa
EC 编号 ec_number	2.7.1.40,2.7.11.1,2.7.10.2
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	35355

MSKSHSEAGSAFIQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVETLKEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVDVGSKVYVDDGLISLQVKQKGPDFLVTEVENGGFLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKILGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMIIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAMFHRKLFEELARASSHSTDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQEAWAEDVDLRVNLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	SUCCINIC ACID
Molecular weight formula_weight	118.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	nat
Copy count entity_count	15

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	ALANINE
Molecular weight formula_weight	89.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	26

Entity 8 Entity 8 non-polymer

Description description	(E)-2-METHYL-3-PHOSPHONOACRYLATE
Molecular weight formula_weight	166.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2882

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Unit-cell length a length_a	93.026 Å
Unit-cell length b length_b	216.396 Å
Unit-cell length c length_c	258.151 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	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	46.020 Å
R factor r_factor	0.1584
R_work r_work	0.1559
R_free r_free	0.2047

Complex of Rabbit muscle pyruvate kinase with ADP and the phosphonate analogue of PEP mimicking the Michaelis complex.

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

8f6m__assembly_1__model_1

8f6m__assembly_1__model_1 | I(q)

8f6m__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)

Complex of Rabbit muscle pyruvate kinase with ADP and the phosphonate analogue of PEP mimicking the Michaelis complex.

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

8f6m__assembly_1__model_1

8f6m__assembly_1__model_1 | I(q)

8f6m__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)