SAXSdb — 1pvn

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

;Inosine-5'-monophosphate dehydrogenase ;

Tritrichomonas foetus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	POTASSIUM ION × 8 4-CARBAMOYL-1-BETA-D-RIBOFURANOSYL-IMIDAZOLIUM-5-OLATE-5'-PHOSPHATE × 4 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IMDH_TRIFO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 2–100 Author chain A； PDBConstruct 100–376； UniProt 227–503 Author chain B； PDBConstruct 1–99； UniProt 2–100 Author chain B； PDBConstruct 100–376； UniProt 227–503 Author chain C； PDBConstruct 1–99； UniProt 2–100 Author chain C； PDBConstruct 100–376； UniProt 227–503 Author chain D； PDBConstruct 1–99； UniProt 2–100 Author chain D； PDBConstruct 100–376； UniProt 227–503

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	1pvn
Deposition date deposition_date	2003-06-27
Structure title title	The crystal structure of the complex between IMP dehydrogenase catalytic domain and a transition state analogue MZP
Keywords keywords	;Transition state analogue, IMP dehydrogenase, Mizoribine 5'-monophosphate, distal flap, general base, drug selectivity, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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.

1pvn__assembly_1__model_1

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

Download this curve (.dat)

1pvn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pvn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.16 Å
Rg (electron density)	35.54 Å
Total Rg	35.97 Å
Atom count	11228
Residues	1448
Excluded volume	200800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pvn__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 (5)

Entity 1 Entity 1 polymer

Description description	;Inosine-5'-monophosphate dehydrogenase ;
Molecular weight formula_weight	41212.9 kDa
EC 编号 ec_number	1.1.1.205
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	12198

AKYYNEPCHTFNEYLLIPGLSTVDCIPSNVNLSTPLVKFQKGQQSEINLKIPLVSAIMQSVSGEKMAIALAREGGISFIFGSQSIESQAAMVHAVKNFKDSQKRYLVGAGINTRDFRERVPALVEAGADVLCIDSSDGFSEWQKITIGWIREKYGDKVKVGAGNIVDGEGFRYLADAGADFIKIGIGGGSICITREQKGIGRGQATAVIDVVAERNKYFEETGIYIPVCSDGGIVYDYHMTLALAMGADFIMLGRYFARFEESPTRKVTINGSVMKEYWGEGSSRARNWQRYDLGGKQKLSFEEGVDSYVPYAGKLKDNVEASLNKVKSTMCNCGALTIPQLQSKAKITLVSSVSIVEGGAHDVIVKDRINDYHPK

Source Source

Source organism organism	Tritrichomonas foetus
NCBI taxonomy ID ncbi_taxonomy_id	5724
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	4-CARBAMOYL-1-BETA-D-RIBOFURANOSYL-IMIDAZOLIUM-5-OLATE-5'-PHOSPHATE
Molecular weight formula_weight	337.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	970

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1pvna1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.5 — Inosine monophosphate dehydrogenase (IMPDH)
Family Family family	c.1.5.1 — Inosine monophosphate dehydrogenase (IMPDH)

Domain ID domain_id	d1pvnb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.5 — Inosine monophosphate dehydrogenase (IMPDH)
Family Family family	c.1.5.1 — Inosine monophosphate dehydrogenase (IMPDH)

Domain ID domain_id	d1pvnc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.5 — Inosine monophosphate dehydrogenase (IMPDH)
Family Family family	c.1.5.1 — Inosine monophosphate dehydrogenase (IMPDH)

Domain ID domain_id	d1pvnd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.5 — Inosine monophosphate dehydrogenase (IMPDH)
Family Family family	c.1.5.1 — Inosine monophosphate dehydrogenase (IMPDH)

CATH v4.4 (4 domains)

Domain ID domain_id	1pvnA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1pvnB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1pvnC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1pvnD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	96.754 Å
Unit-cell length b length_b	112.566 Å
Unit-cell length c length_c	159.756 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	2.000 Å
Low-resolution limit resolution_low	29.710 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2220

The crystal structure of the complex between IMP dehydrogenase catalytic domain and a transition state analogue MZP

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

;Inosine-5'-monophosphate dehydrogenase ;

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

1pvn__assembly_1__model_1

1pvn__assembly_1__model_1 | I(q)

1pvn__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

The crystal structure of the complex between IMP dehydrogenase catalytic domain and a transition state analogue MZP

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

;Inosine-5'-monophosphate dehydrogenase ;

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

1pvn__assembly_1__model_1

1pvn__assembly_1__model_1 | I(q)

1pvn__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)