1wyu

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form

Method: X-RAY DIFFRACTION

▼

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

glycine dehydrogenase (decarboxylating) subunit 1

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	glycine dehydrogenase subunit 2 (P-protein) × 2 （Q5SKW7） PYRIDOXAL-5'-PHOSPHATE × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	glycine dehydrogenase subunit 2 (P-protein) × 2 （Q5SKW7） PYRIDOXAL-5'-PHOSPHATE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SKW8_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–438； UniProt 1–438 Author chain C； PDBConstruct 1–438； UniProt 1–438 Author chain E； PDBConstruct 1–438； UniProt 1–438 Author chain G； PDBConstruct 1–438； UniProt 1–438

glycine dehydrogenase subunit 2 (P-protein)

Thermus thermophilus

UniProt Q5SKW7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	glycine dehydrogenase (decarboxylating) subunit 1 × 2 （Q5SKW8） PYRIDOXAL-5'-PHOSPHATE × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	glycine dehydrogenase (decarboxylating) subunit 1 × 2 （Q5SKW8） PYRIDOXAL-5'-PHOSPHATE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SKW7_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–474； UniProt 1–474 Author chain D； PDBConstruct 1–474； UniProt 1–474 Author chain F； PDBConstruct 1–474； UniProt 1–474 Author chain H； PDBConstruct 1–474； UniProt 1–474

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1wyu
Deposition date deposition_date	2005-02-17
Structure title title	Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form
Keywords keywords	ALPHA(2)BETA(2) TETRAMER, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1wyu__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1wyu__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wyu__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.75 Å
Rg (electron density)	34.91 Å
Total Rg	35.52 Å
Atom count	14096
Residues	1820
Excluded volume	252350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wyu__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wyu__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	glycine dehydrogenase (decarboxylating) subunit 1
Molecular weight formula_weight	47168.1 kDa
EC 编号 ec_number	1.4.4.2
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	30337

MDYTPHTEEEIREMLRRVGAASLEDLFAHLPKEILSPPIDLPEPLPEWKVLEELRRLAAQNLPAHKAFLGGGVRSHHVPPVVQALAARGEFLTAYTPYQPEVSQGVLQATFEYQTMIAELAGLEIANASMYDGATALAEGVLLALRETGRMGVLVSQGVHPEYRAVLRAYLEAVGAKLLTLPLEGGRTPLPEVGEEVGAVVVQNPNFLGALEDLGPFAEAAHGAGALFVAVADPLSLGVLKPPGAYGADIAVGDGQSLGLPMGFGGPHFGFLATKKAFVRQLPGRLVSETVDVEGRRGFILTLQAREQYIRRAKAKSNITTNAQLTALMGAMYLAALGPEGLREVALKSVEMAHKLHALLLEVPGVRPFTPKPFFNEFALALPKDPEAVRRALAERGFHGATPVPREYGENLALFAATELHEEEDLLALREALKEVLA

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	glycine dehydrogenase subunit 2 (P-protein)
Molecular weight formula_weight	52784.7 kDa
EC 编号 ec_number	1.4.4.2
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MSFPLIFERSRKGRRGLKLVKAVPKAEDLIPKEHLREVPPRLPEVDELTLVRHYTGLSRRQVGVDTTFYPLGSCTMKYNPKLHEEAARLFADLHPYQDPRTAQGALRLMWELGEYLKALTGMDAITLEPAAGAHGELTGILIIRAYHEDRGEGRTRRVVLVPDSAHGSNPATASMAGYQVREIPSGPEGEVDLEALKRELGPHVAALMLTNPNTLGLFERRILEISRLCKEAGVQLYYDGANLNAIMGWARPGDMGFDVVHLNLHKTFTVPHGGGGPGSGPVGVKAHLAPYLPVPLVERGEEGFYLDFDRPKSIGRVRSFYGNFLALVRAWAYIRTLGLEGLKKAAALAVLNARYLKELLKEKGYRVPYDGPSMHEFVAQPPEGFRALDLAKGLLELGFHPPTVYFPLIVKEALMVEPTETEAKETLEAFAEAMGALLKKPKEWLENAPYSTPVRRLDELRANKHPKLTYFDEG

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 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	2145

▼

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1wyua_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

Domain ID domain_id	d1wyub_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

Domain ID domain_id	d1wyuc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

Domain ID domain_id	d1wyud_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

Domain ID domain_id	d1wyue_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

Domain ID domain_id	d1wyuf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

Domain ID domain_id	d1wyug_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

Domain ID domain_id	d1wyuh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.7 — Glycine dehydrogenase subunits (GDC-P)

CATH v4.4 (20 domains)

Domain ID domain_id	1wyuA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1wyuA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1wyuB01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	440 — Translocated Intimin Receptor; Chain T
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1wyuB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1wyuB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1wyuC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1wyuC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1wyuD01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	440 — Translocated Intimin Receptor; Chain T
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1wyuD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1wyuD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1wyuE01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1wyuE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1wyuF01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	440 — Translocated Intimin Receptor; Chain T
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1wyuF02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1wyuF03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1wyuG01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1wyuG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1wyuH01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	440 — Translocated Intimin Receptor; Chain T
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1wyuH02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1wyuH03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

▶

Unit-cell length a length_a	134.874 Å
Unit-cell length b length_b	166.673 Å
Unit-cell length c length_c	189.007 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	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	49.570 Å
R factor r_factor	0.1910
R_work r_work	0.1890
R_free r_free	0.2290

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form

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

glycine dehydrogenase (decarboxylating) subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

glycine dehydrogenase subunit 2 (P-protein)

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

1wyu__assembly_2__model_1

1wyu__assembly_2__model_1 | I(q)

1wyu__assembly_2__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (8 domains)

CATH v4.4 (20 domains)

7. Citations (1)

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form

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

glycine dehydrogenase (decarboxylating) subunit 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

glycine dehydrogenase subunit 2 (P-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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1wyu__assembly_2__model_1

1wyu__assembly_2__model_1 | I(q)

1wyu__assembly_2__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (8 domains)

CATH v4.4 (20 domains)

7. Citations (1)