SAXSdb — 1im5

▼

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

180aa long hypothetical Pyrazinamidase/Nicotinamidase

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O58727_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–180； UniProt 1–180

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	1im5
Deposition date deposition_date	2001-05-09
Structure title title	Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc
Keywords keywords	;pyrazinamidase, pyrazinamide, nicotinamidase, tuberculosis, PZA resistance, drug resistance, metal ion catalysis, cysteine hydrolase, hydrolase, amidase, covalent catalysis ;; HYDROLASE
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.

1im5__assembly_1__model_1

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

Download this curve (.dat)

1im5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1im5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.77 Å
Rg (electron density)	15.41 Å
Total Rg	16.44 Å
Atom count	1414
Residues	179
Excluded volume	25253 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1im5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	180aa long hypothetical Pyrazinamidase/Nicotinamidase
Molecular weight formula_weight	20222.2 kDa
EC 编号 ec_number	3.5.1.19
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	1566

MPEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATRDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKEAYSGFEGTDLAKILRGNGVKRVYICGVATEYCVRATALDALKHGFEVYLLRDAVKGIKPEDEERALEEMKSRGIKIVQF

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1im5a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.33 — Isochorismatase-like hydrolases
Superfamily Superfamily superfamily	c.33.1 — Isochorismatase-like hydrolases
Family Family family	c.33.1.3 — Isochorismatase-like hydrolases

CATH v4.4 (1 domains)

Domain ID domain_id	1im5A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	850 — Isochorismatase-like

▶

Unit-cell length a length_a	32.978 Å
Unit-cell length b length_b	43.266 Å
Unit-cell length c length_c	55.553 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1529
R_work r_work	0.1527
R_free r_free	0.2323

Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc

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

180aa long hypothetical Pyrazinamidase/Nicotinamidase

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

1im5__assembly_1__model_1

1im5__assembly_1__model_1 | I(q)

1im5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc

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

180aa long hypothetical Pyrazinamidase/Nicotinamidase

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

1im5__assembly_1__model_1

1im5__assembly_1__model_1 | I(q)

1im5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)