6efg

Pyruvate decarboxylase from Kluyveromyces lactis

Method: X-RAY DIFFRACTION

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

Pyruvate decarboxylase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	THIAMINE DIPHOSPHATE × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	THIAMINE DIPHOSPHATE × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDC1_KLULA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–563； UniProt 1–563 Author chain B； PDBConstruct 1–563； UniProt 1–563 Author chain D； PDBConstruct 1–563； UniProt 1–563 Author chain E； PDBConstruct 1–563； UniProt 1–563

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	6efg
Deposition date deposition_date	2018-08-16
Structure title title	Pyruvate decarboxylase from Kluyveromyces lactis
Keywords keywords	pyruvate decarboxylase, thiamine diphosphate, substrate activation, LYASE; LYASE
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.

6efg__assembly_1__model_1

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

Download this curve (.dat)

6efg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6efg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.37 Å
Rg (electron density)	30.78 Å
Total Rg	31.44 Å
Atom count	8290
Residues	1068
Excluded volume	147970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6efg__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6efg__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Pyruvate decarboxylase
Molecular weight formula_weight	61716.8 kDa
EC 编号 ec_number	4.1.1.1
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	16950

MSEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANELNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTAATNAKN

Entity 2 Entity 2 non-polymer

Description description	THIAMINE DIPHOSPHATE
Molecular weight formula_weight	425.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	308

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6efga1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d6efga2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.0 — automated matches

Domain ID domain_id	d6efga3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d6efgb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d6efgb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.0 — automated matches

Domain ID domain_id	d6efgb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d6efgd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d6efgd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.0 — automated matches

Domain ID domain_id	d6efgd3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d6efge1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d6efge2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.0 — automated matches

Domain ID domain_id	d6efge3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	6efgA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	6efgA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	6efgA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	6efgB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	6efgB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	6efgB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	6efgD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	6efgD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	6efgD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	6efgE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	6efgE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	6efgE03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

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Unit-cell length a length_a	78.360 Å
Unit-cell length b length_b	78.480 Å
Unit-cell length c length_c	100.570 Å
Unit-cell angle α angle_alpha	80.10 °
Unit-cell angle β angle_beta	67.72 °
Unit-cell angle γ angle_gamma	77.40 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.040 Å
Low-resolution limit resolution_low	38.250 Å
R factor r_factor	0.2212
R_work r_work	0.2207
R_free r_free	0.2903

Pyruvate decarboxylase from Kluyveromyces lactis

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

Pyruvate decarboxylase

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

6efg__assembly_1__model_1

6efg__assembly_1__model_1 | I(q)

6efg__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (2)

Pyruvate decarboxylase from Kluyveromyces lactis

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

Pyruvate decarboxylase

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

6efg__assembly_1__model_1

6efg__assembly_1__model_1 | I(q)

6efg__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (2)