1wyv

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

Method: X-RAY DIFFRACTION

▼

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

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein heterocomplex	Heteromer	4 / 0 / 0 / 0	Consistent with protein count
2	Protein heterocomplex	Heteromer	4 / 0 / 0 / 0	Consistent with protein count

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	1wyv
Deposition date deposition_date	2005-02-17
Structure title title	Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound 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.

1wyv__assembly_2__model_1

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

Download this curve (.dat)

1wyv__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wyv__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.76 Å
Rg (electron density)	34.92 Å
Total Rg	35.53 Å
Atom count	14108
Residues	1820
Excluded volume	252530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wyv__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wyv__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 (5)

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	29408

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 non-polymer

Description description	(AMINOOXY)ACETIC ACID
Molecular weight formula_weight	91.1 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	1192

▼

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1wyva_
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	d1wyvb_
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	d1wyvc_
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	d1wyvd_
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	d1wyve_
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	d1wyvf_
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	d1wyvg_
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	d1wyvh_
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	1wyvA01
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	1wyvA02
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	1wyvB01
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	1wyvB02
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	1wyvB03
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	1wyvC01
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	1wyvC02
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	1wyvD01
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	1wyvD02
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	1wyvD03
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	1wyvE01
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	1wyvE02
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	1wyvF01
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	1wyvF02
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	1wyvF03
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	1wyvG01
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	1wyvG02
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	1wyvH01
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	1wyvH02
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	1wyvH03
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	134.173 Å
Unit-cell length b length_b	166.317 Å
Unit-cell length c length_c	190.299 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	2.400 Å
Low-resolution limit resolution_low	47.900 Å
R factor r_factor	0.1900
R_work r_work	0.1880
R_free r_free	0.2300

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

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

Assembly Composition of the Current Entry

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1wyv__assembly_2__model_1

1wyv__assembly_2__model_1 | I(q)

1wyv__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (8 domains)

CATH v4.4 (20 domains)

7. Citations (1)