1i48

CYSTATHIONINE GAMMA-SYNTHASE IN COMPLEX WITH THE INHIBITOR CTCPO

Method: X-RAY DIFFRACTION

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

CYSTATHIONINE GAMMA-SYNTHASE

Nicotiana tabacum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PYRIDOXAL-5'-PHOSPHATE × 4 CARBOXYMETHYLTHIO-3-(3-CHLOROPHENYL)-1,2,4-OXADIAZOL × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	PYRIDOXAL-5'-PHOSPHATE × 4 CARBOXYMETHYLTHIO-3-(3-CHLOROPHENYL)-1,2,4-OXADIAZOL × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	PYRIDOXAL-5'-PHOSPHATE × 4 CARBOXYMETHYLTHIO-3-(3-CHLOROPHENYL)-1,2,4-OXADIAZOL × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9ZPL5_TOBAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–445； UniProt 1–445 Author chain B； PDBConstruct 1–445； UniProt 1–445 Author chain C； PDBConstruct 1–445； UniProt 1–445 Author chain D； PDBConstruct 1–445； UniProt 1–445 Author chain E； PDBConstruct 1–445； UniProt 1–445 Author chain F； PDBConstruct 1–445； UniProt 1–445 Author chain G； PDBConstruct 1–445； UniProt 1–445 Author chain H； PDBConstruct 1–445； UniProt 1–445 Author chain I； PDBConstruct 1–445； UniProt 1–445 Author chain J； PDBConstruct 1–445； UniProt 1–445 Author chain K； PDBConstruct 1–445； UniProt 1–445 Author chain L； PDBConstruct 1–445； UniProt 1–445

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	1i48
Deposition date deposition_date	2001-02-20
Structure title title	CYSTATHIONINE GAMMA-SYNTHASE IN COMPLEX WITH THE INHIBITOR CTCPO
Keywords keywords	PLP-dependent enzyme, homotetramer, inhibitor complex, CTCPO, 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.

1i48__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1i48__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1i48__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	34.20 Å
Rg (electron density)	33.48 Å
Total Rg	34.08 Å
Atom count	12220
Residues	1584
Excluded volume	219050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1i48__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1i48__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1i48__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Description description	CYSTATHIONINE GAMMA-SYNTHASE
Molecular weight formula_weight	48068.0 kDa
EC 编号 ec_number	4.2.99.9
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	36660

MAKAVDAAAAAAAAIAPVDTTVVNEDVALVENETCNDQNVQFDSLPSMKYASFLNSDGSVAIHAGERLGRGIVTDAITTPVVNTSAYFFNKTSELIDFKEKRRASFEYGRYGNPTTVVLEEKISALEGAESTLLMASGMCASTVMLLALVPAGGHIVTTTDCYRKTRIFIETILPKMGITATVIDPADVGALELALNQKKVNLFFTESPTNPFLRCVDIELVSKLCHEKGALVCIDGTFATPLNQKALALGADLVLHSATKFLGGHNDVLAGCISGPLKLVSEIRNLHHILGGALNPNAAYLIIRGMKTLHLRVQQQNSTALRMAEILEAHPKVRHVYYPGLQSHPEHHIAKKQMTGFGGAVSFEVDGDLLTTAKFVDALKIPYIAPSFGGCESIVDQPAIMSYWDLSQSDRAKYGIMDNLVRFSFGVEDFDDLKADILQALDSI

Source Source

Source organism organism	Nicotiana tabacum
Common name common_name	common tobacco
NCBI taxonomy ID ncbi_taxonomy_id	4097
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	CARBOXYMETHYLTHIO-3-(3-CHLOROPHENYL)-1,2,4-OXADIAZOL
Molecular weight formula_weight	270.7 kDa
Source method src_method	syn
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1i48a_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48b_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48c_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48d_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48e_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48f_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48g_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48h_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48i_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48j_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48k_
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.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d1i48l_
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.67.1.3 — Cystathionine synthase-like

CATH v4.4 (24 domains)

Domain ID domain_id	1i48A01
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	1i48A02
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	1i48B01
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	1i48B02
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	1i48C01
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	1i48C02
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	1i48D01
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	1i48D02
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	1i48E01
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	1i48E02
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	1i48F01
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	1i48F02
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	1i48G01
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	1i48G02
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	1i48H01
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	1i48H02
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	1i48I01
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	1i48I02
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	1i48J01
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	1i48J02
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	1i48K01
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	1i48K02
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	1i48L01
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	1i48L02
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

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Unit-cell length a length_a	312.400 Å
Unit-cell length b length_b	165.600 Å
Unit-cell length c length_c	162.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2260
R_free r_free	0.2570

CYSTATHIONINE GAMMA-SYNTHASE IN COMPLEX WITH THE INHIBITOR CTCPO

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

CYSTATHIONINE GAMMA-SYNTHASE

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

1i48__assembly_3__model_1

1i48__assembly_3__model_1 | I(q)

1i48__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. Citations (1)

CYSTATHIONINE GAMMA-SYNTHASE IN COMPLEX WITH THE INHIBITOR CTCPO

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

CYSTATHIONINE GAMMA-SYNTHASE

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

1i48__assembly_3__model_1

1i48__assembly_3__model_1 | I(q)

1i48__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. Citations (1)