SAXSdb — 1ugp

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

Cobalt-containing nitrile hydratase subunit alpha

Pseudonocardia thermophila

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cobalt-containing nitrile hydratase subunit beta × 1 （Q7SID3） COBALT (II) ION × 1 butanoic acid × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cobalt-containing nitrile hydratase subunit beta × 2 （Q7SID3） COBALT (II) ION × 2 butanoic acid × 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 1–203； UniProt 2–204

Cobalt-containing nitrile hydratase subunit beta

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 2	Cobalt-containing nitrile hydratase subunit alpha × 1 （Q7SID2） COBALT (II) ION × 1 butanoic acid × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Cobalt-containing nitrile hydratase subunit alpha × 2 （Q7SID2） COBALT (II) ION × 2 butanoic acid × 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 1–226； UniProt 1–226

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	1ugp
Deposition date deposition_date	2003-06-17
Structure title title	Crystal structure of Co-type nitrile hydratase complexed with n-butyric acid
Keywords keywords	COMPLEX, N-BUTYRIC ACID, 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.

1ugp__assembly_2__model_1

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

Download this curve (.dat)

1ugp__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ugp__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.91 Å
Rg (electron density)	29.21 Å
Total Rg	29.88 Å
Atom count	6920
Residues	854
Excluded volume	122490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ugp__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ugp__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Cobalt-containing nitrile hydratase subunit alpha
Molecular weight formula_weight	23088.4 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	3863

TENILRKSDEEIQKEITARVKALESMLIEQGILTTSMIDRMAEIYENEVGPHLGAKVVVKAWTDPEFKKRLLADGTEACKELGIGGLQGEDMMWVENTDEVHHVVVCTLCSCYPWPVLGLPPNWFKEPQYRSRVVREPRQLLKEEFGFEVPPSKEIKVWDSSSEMRFVVLPQRPAGTDGWSEEELATLVTRESMIGVEPAKAV

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	Cobalt-containing nitrile hydratase subunit beta
Molecular weight formula_weight	25954.0 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

MNGVYDVGGTDGLGPINRPADEPVFRAEWEKVAFAMFPATFRAGFMGLDEFRFGIEQMNPAEYLESPYYWHWIRTYIHHGVRTGKIDLEELERRTQYYRENPDAPLPEHEQKPELIEFVNQAVYGGLPASREVDRPPKFKEGDVVRFSTASPKGHARRARYVRGKTGTVVKHHGAYIYPDTAGNGLGECPEHLYTVRFTAQELWGPEGDPNSSVYYDCWEPYIELV

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 non-polymer

Description description	butanoic acid
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	397

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ugpa_
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	d1ugpb_
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	1ugpA00
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	1ugpB01
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	1ugpB02
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	65.564 Å
Unit-cell length b length_b	65.564 Å
Unit-cell length c length_c	184.994 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	1.630 Å
Low-resolution limit resolution_low	24.540 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.1970

Crystal structure of Co-type nitrile hydratase complexed with n-butyric acid

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

Cobalt-containing nitrile hydratase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Cobalt-containing nitrile hydratase subunit beta

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

1ugp__assembly_2__model_1

1ugp__assembly_2__model_1 | I(q)

1ugp__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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Co-type nitrile hydratase complexed with n-butyric acid

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

Cobalt-containing nitrile hydratase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cobalt-containing nitrile hydratase subunit beta

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

1ugp__assembly_2__model_1

1ugp__assembly_2__model_1 | I(q)

1ugp__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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)