2ihv

Carboxyethylarginine synthase from Streptomyces clavuligerus: 5-guanidinovaleric acid complex

Method: X-RAY DIFFRACTION

▼

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

Carboxyethylarginine synthase

Streptomyces clavuligerus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 POTASSIUM ION × 6 THIAMINE DIPHOSPHATE × 4 5-{[AMINO(IMINO)METHYL]AMINO}PENTANOIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9LCV9_STRCL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–573； UniProt 1–573 Author chain B； PDBConstruct 1–573； UniProt 1–573 Author chain C； PDBConstruct 1–573； UniProt 1–573 Author chain D； PDBConstruct 1–573； UniProt 1–573

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	2ihv
Deposition date deposition_date	2006-09-27
Structure title title	Carboxyethylarginine synthase from Streptomyces clavuligerus: 5-guanidinovaleric acid complex
Keywords keywords	Thiamin diphosphate complex, Transferase; TRANSFERASE
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.

2ihv__assembly_1__model_1

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

Download this curve (.dat)

2ihv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ihv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.49 Å
Rg (electron density)	37.62 Å
Total Rg	38.05 Å
Atom count	16980
Residues	2240
Excluded volume	301900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ihv__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	Carboxyethylarginine synthase
Molecular weight formula_weight	60964.8 kDa
EC 编号 ec_number	2.5.1.66
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	18002

MSRVSTAPSGKPTAAHALLSRLRDHGVGKVFGVVGREAASILFDEVEGIDFVLTRHEFTAGVAADVLARITGRPQACWATLGPGMTNLSTGIATSVLDRSPVIALAAQSESHDIFPNDTHQCLDSVAIVAPMSKYAVELQRPHEITDLVDSAVNAAMTEPVGPSFISLPVDLLGSSEGIDTTVPNPPANTPAKPVGVVADGWQKAADQAAALLAEAKHPVLVVGAAAIRSGAVPAIRALAERLNIPVITTYIAKGVLPVGHELNYGAVTGYMDGILNFPALQTMFAPVDLVLTVGYDYAEDLRPSMWQKGIEKKTVRISPTVNPIPRVYRPDVDVVTDVLAFVEHFETATASFGAKQRHDIEPLRARIAEFLADPETYEDGMRVHQVIDSMNTVMEEAAEPGEGTIVSDIGFFRHYGVLFARADQPFGFLTSAGCSSFGYGIPAAIGAQMARPDQPTFLIAGDGGFHSNSSDLETIARLNLPIVTVVVNNDTNGLIELYQNIGHHRSHDPAVKFGGVDFVALAEANGVDATRATNREELLAALRKGAELGRPFLIEVPVNYDFQPGGFGALSI

Source Source

Source organism organism	Streptomyces clavuligerus
NCBI taxonomy ID ncbi_taxonomy_id	1901
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	5-{[AMINO(IMINO)METHYL]AMINO}PENTANOIC ACID
Molecular weight formula_weight	159.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	990

▼

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2ihva1
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.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain

Domain ID domain_id	d2ihva2
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.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module

Domain ID domain_id	d2ihva3
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.36.1.9 — Pyruvate oxidase and decarboxylase PP module

Domain ID domain_id	d2ihvb1
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.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain

Domain ID domain_id	d2ihvb2
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.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module

Domain ID domain_id	d2ihvb3
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.36.1.9 — Pyruvate oxidase and decarboxylase PP module

Domain ID domain_id	d2ihvc1
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.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module

Domain ID domain_id	d2ihvc2
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.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain

Domain ID domain_id	d2ihvc3
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.36.1.9 — Pyruvate oxidase and decarboxylase PP module

Domain ID domain_id	d2ihvd1
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.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain

Domain ID domain_id	d2ihvd2
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.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module

Domain ID domain_id	d2ihvd3
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.36.1.9 — Pyruvate oxidase and decarboxylase PP module

CATH v4.4 (12 domains)

Domain ID domain_id	2ihvA01
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	2ihvA02
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	2ihvA03
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	2ihvB01
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	2ihvB02
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	2ihvB03
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	2ihvC01
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	2ihvC02
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	2ihvC03
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	2ihvD01
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	2ihvD02
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	2ihvD03
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

▶

Unit-cell length a length_a	120.744 Å
Unit-cell length b length_b	128.297 Å
Unit-cell length c length_c	197.638 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	2.300 Å
Low-resolution limit resolution_low	49.150 Å
R factor r_factor	0.1620
R_work r_work	0.1610
R_free r_free	0.1920

Carboxyethylarginine synthase from Streptomyces clavuligerus: 5-guanidinovaleric acid complex

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

Carboxyethylarginine 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

2ihv__assembly_1__model_1

2ihv__assembly_1__model_1 | I(q)

2ihv__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Carboxyethylarginine synthase from Streptomyces clavuligerus: 5-guanidinovaleric acid complex

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

Carboxyethylarginine 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

2ihv__assembly_1__model_1

2ihv__assembly_1__model_1 | I(q)

2ihv__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)