SAXSdb — 1ire

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

Nitrile Hydratase

Pseudonocardia thermophila

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Nitrile Hydratase × 2 （Q7SID3） COBALT (II) ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHAA_PSETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–204； UniProt 1–203

Nitrile Hydratase

Pseudonocardia thermophila

UniProt Q7SID3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Nitrile Hydratase × 2 （Q7SID2） COBALT (II) ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHAB_PSETH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–228； UniProt 1–228

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	1ire
Deposition date deposition_date	2001-10-01
Structure title title	Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila
Keywords keywords	Cysteine-sulfinic acid, cysteine-sulfenic acid, post-translational modification, non-corrin cobalt, nitrile, hydration, 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.

1ire__assembly_1__model_1

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

Download this curve (.dat)

1ire__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ire__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.97 Å
Rg (electron density)	29.25 Å
Total Rg	29.94 Å
Atom count	6938
Residues	858
Excluded volume	122720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ire__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Nitrile Hydratase
Molecular weight formula_weight	23219.6 kDa
EC 编号 ec_number	4.2.1.84
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3793

MTENILRKSDEEIQKEITARVKALESMLIEQGILTTSMIDRMAEIYENEVGPHLGAKVVVKAWTDPEFKKRLLADGTEACKELGIGGLQGEDMMWVENTDEVHHVVVCTLCSCYPWPVLGLPPNWFKEPQYRSRVVREPRQLLKEEFGFEVPPSKEIKVWDSSSEMRFVVLPQRPAGTDGWSEEELATLVTRESMIGVEPAKAV

Source Source

Source organism organism	Pseudonocardia thermophila
NCBI taxonomy ID ncbi_taxonomy_id	1848
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nitrile Hydratase
Molecular weight formula_weight	26170.1 kDa
EC 编号 ec_number	4.2.1.84
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNGVYDVGGTDGLGPINRPADEPVFRAEWEKVAFAMFPATFRAGFMGLDEFRFGIEQMNPAEYLESPYYWHWIRTYIHHGVRTGKIDLEELERRTQYYRENPDAPLPEHEQKPELIEFVNQAVYGGLPASREVDRPPKFKEGDVVRFSTASPKGHARRARYVRGKTGTVVKHHGAYIYPDTAGNGLGECPEHLYTVRFTAQELWGPEGDPNSSVYYDCWEPYIELVDT

Source Source

Source organism organism	Pseudonocardia thermophila
NCBI taxonomy ID ncbi_taxonomy_id	1848
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	324

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1irea_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.149 — Nitrile hydratase alpha chain
Superfamily Superfamily superfamily	d.149.1 — Nitrile hydratase alpha chain
Family Family family	d.149.1.1 — Nitrile hydratase alpha chain

Domain ID domain_id	d1ireb_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.4 — Electron transport accessory proteins
Family Family family	b.34.4.4 — Nitrile hydratase beta chain

CATH v4.4 (3 domains)

Domain ID domain_id	1ireA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	330 — Nitrile Hydratase; Chain A
Homologous superfamily homologous superfamily	10 — Nitrile hydratase alpha /Thiocyanate hydrolase gamma

Domain ID domain_id	1ireB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	20 — Nitrile hydratase, beta subunit

Domain ID domain_id	1ireB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	65.501 Å
Unit-cell length b length_b	65.501 Å
Unit-cell length c length_c	184.614 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	28.030 Å
R factor r_factor	0.1786
R_work r_work	0.1781
R_free r_free	0.1905

Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila

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

Nitrile Hydratase

State in the Current Structure

Other States of the Same Protein in the Database

Nitrile Hydratase

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

1ire__assembly_1__model_1

1ire__assembly_1__model_1 | I(q)

1ire__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

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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (2)

Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila

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

Nitrile Hydratase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nitrile Hydratase

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

1ire__assembly_1__model_1

1ire__assembly_1__model_1 | I(q)

1ire__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

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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (2)