SAXSdb — 2zpf

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

Nitrile hydratase subunit alpha

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nitrile hydratase subunit beta × 1 （P13449） FE (III) ION × 1 NITRIC OXIDE × 1 MAGNESIUM ION × 4 tert-butyl isocyanide × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Nitrile hydratase subunit beta × 2 （P13449） FE (III) ION × 2 NITRIC OXIDE × 2 MAGNESIUM ION × 8 tert-butyl isocyanide × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHAA_RHOER
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–206； UniProt 2–207

Nitrile hydratase subunit beta

OrganismNot specified

UniProt P13449

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nitrile hydratase subunit alpha × 1 （P13448） FE (III) ION × 1 NITRIC OXIDE × 1 MAGNESIUM ION × 4 tert-butyl isocyanide × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Nitrile hydratase subunit alpha × 2 （P13448） FE (III) ION × 2 NITRIC OXIDE × 2 MAGNESIUM ION × 8 tert-butyl isocyanide × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHAB_RHOER
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–212； UniProt 1–212

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	2zpf
Deposition date deposition_date	2008-07-11
Structure title title	Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 18min at 293K
Keywords keywords	LYASE, Iron, Metal-binding, Oxidation; 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.

2zpf__assembly_2__model_1

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

Download this curve (.dat)

2zpf__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zpf__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.96 Å
Rg (electron density)	28.26 Å
Total Rg	28.88 Å
Atom count	6408
Residues	810
Excluded volume	113420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zpf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zpf__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 (7)

Entity 1 Entity 1 polymer

Description description	Nitrile hydratase subunit alpha
Molecular weight formula_weight	22933.9 kDa
EC 编号 ec_number	4.2.1.84
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3909

SVTIDHTTENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLCSCTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPTV

Entity 2 Entity 2 polymer

Description description	Nitrile hydratase subunit beta
Molecular weight formula_weight	23514.3 kDa
EC 编号 ec_number	4.2.1.84
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVRYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPAA

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	NITRIC OXIDE
Molecular weight formula_weight	30.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	tert-butyl isocyanide
Molecular weight formula_weight	83.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	643

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2zpfa_
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	d2zpfb_
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	2zpfA00
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	2zpfB01
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	2zpfB02
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	114.045 Å
Unit-cell length b length_b	59.995 Å
Unit-cell length c length_c	81.710 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	125.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.482 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1688
R_work r_work	0.1677
R_free r_free	0.1895

Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 18min at 293K

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

Nitrile hydratase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

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

2zpf__assembly_2__model_1

2zpf__assembly_2__model_1 | I(q)

2zpf__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 18min at 293K

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

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

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

2zpf__assembly_2__model_1

2zpf__assembly_2__model_1 | I(q)

2zpf__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)