2b1g

Crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase

Method: X-RAY DIFFRACTION

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

Bifunctional purine biosynthesis protein PURH

Gallus gallus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 1 POTASSIUM ION × 2 7-(3,4-DIHYDROXY-5R-HYDROXYMETHYLTETRAHYDROFURAN-2-YL)-2,2-DIOXO-1,2R,3R,7-TETRAHYDRO-2L6-IMIDAZO[4,5-C][1,2,6]THIADIAZIN-4S-ONE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 1 POTASSIUM ION × 2 7-(3,4-DIHYDROXY-5R-HYDROXYMETHYLTETRAHYDROFURAN-2-YL)-2,2-DIOXO-1,2R,3R,7-TETRAHYDRO-2L6-IMIDAZO[4,5-C][1,2,6]THIADIAZIN-4S-ONE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PUR9_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–593； UniProt 1–593 Author chain B； PDBConstruct 1–593； UniProt 1–593 Author chain C； PDBConstruct 1–593； UniProt 1–593 Author chain D； PDBConstruct 1–593； UniProt 1–593

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	2b1g
Deposition date deposition_date	2005-09-15
Structure title title	Crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase
Keywords keywords	ATIC, IMPCH, structure-base, transition state analogue, inhibitor, TRANSFERASE, HYDROLASE; TRANSFERASE, HYDROLASE
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.

2b1g__assembly_1__model_1

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

Download this curve (.dat)

2b1g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2b1g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.37 Å
Rg (electron density)	33.87 Å
Total Rg	34.40 Å
Atom count	9050
Residues	1180
Excluded volume	161370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2b1g__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2b1g__assembly_2__model_1`	dimeric （2）	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	Bifunctional purine biosynthesis protein PURH
Molecular weight formula_weight	64497.7 kDa
EC 编号 ec_number	3.5.4.10, 2.1.2.3
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	18526

MAARQQLALLSVSEKAGLVEFARSLNALGLGLIASGGTATALRDAGLPVRDVSDLTGFPEMLGGRVKTLHPAVHAGILARNIPEDNADMNKQDFSLVRVVVCNLYPFVKTVSSPGVTVPEAVEKIDIGGVALLRAAAKNHARVTVVCDPADYSSVAKEMAASKDKDTSVETRRHLALKAFTHTAQYDAAISDYFRKEYSKGVSQLPLRYGMNPHQSPAQLYTTRPKLPLTVVNGSPGFINLCDALNAWQLVKELKQALGIPAAASFKHVSPAGAAVGIPLSEEEAQVCMVHDLHKTLTPLASAYARSRGADRMSSFGDFIALSDICDVPTAKIISREVSDGVVAPGYEEEALKILSKKKNGGYCVLQMDPNYEPDDNEIRTLYGLQLMQKRNNAVIDRSLFKNIVTKNKTLPESAVRDLIVASIAVKYTQSNSVCYAKDGQVIGIGAGQQSRIHCTRLAGDKANSWWLRHHPRVLSMKFKAGVKRAEVSNAIDQYVTGTIGEDEDLVKWQAMFEEVPAQLTEAEKKQWIAKLTAVSLSSDAFFPFRDNVDRAKRIGVQFIVAPSGSAADEVVIEACNELGITLIHTNLRLFHH

Source Source

Source organism organism	Gallus gallus
Common name common_name	chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	7-(3,4-DIHYDROXY-5R-HYDROXYMETHYLTETRAHYDROFURAN-2-YL)-2,2-DIOXO-1,2R,3R,7-TETRAHYDRO-2L6-IMIDAZO[4,5-C][1,2,6]THIADIAZIN-4S-ONE
Molecular weight formula_weight	320.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	426

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2b1ga1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.3 — Inosicase

Domain ID domain_id	d2b1ga2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.4 — AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC

Domain ID domain_id	d2b1gb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.3 — Inosicase

Domain ID domain_id	d2b1gb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.4 — AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC

Domain ID domain_id	d2b1gc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.3 — Inosicase

Domain ID domain_id	d2b1gc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.4 — AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC

Domain ID domain_id	d2b1gd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.3 — Inosicase

Domain ID domain_id	d2b1gd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.4 — AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC

CATH v4.4 (16 domains)

Domain ID domain_id	2b1gA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	2b1gA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

Domain ID domain_id	2b1gA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

Domain ID domain_id	2b1gA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	2b1gB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	2b1gB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

Domain ID domain_id	2b1gB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

Domain ID domain_id	2b1gB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	2b1gC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	2b1gC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

Domain ID domain_id	2b1gC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

Domain ID domain_id	2b1gC04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	2b1gD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	2b1gD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

Domain ID domain_id	2b1gD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

Domain ID domain_id	2b1gD04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

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7. Citations (8)

;Structure-based Design, Synthesis, Evaluation, and Crystal Structures of Transition State Analogue Inhibitors of Inosine Monophosphate Cyclohydrolase. ;

J.Biol.Chem. (2007)

PMID: 17324932 · DOI: 10.1074/jbc.M607293200 PRIMARY

Crystal structure of avian AICAR transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening

J.Biol.Chem. (2004)

Successful virtual screening for human AICAR transformylase inhibitors against NCI diversity set using AutoDock.

J.Med.Chem. (2004)

Structural insights into the human and avian IMP cyclohydrolase mechanism via crystal structures with the bound XMP Inhibitor

Biochemistry (2004)

;Crystal structures of human bifunctional enzyme aminoimidazole-4-carboxamide ribonucleotide transformylase/IMP cyclohydrolase in complex with potent sulfonyl-containing antifolates ;

J.Biol.Chem. (2004)

Structure of avian AICAR transformylase with a multisubstrate adduct inhibitor beta-DADF identifies the folate binding site

Biochemistry (2003)

Structural insights into the avian AICAR transformylase mechanism

Biochemistry (2002)

Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis

Nat.Struct.Mol.Biol. (2001)

Unit-cell length a length_a	57.200 Å
Unit-cell length b length_b	62.000 Å
Unit-cell length c length_c	196.600 Å
Unit-cell angle α angle_alpha	80.80 °
Unit-cell angle β angle_beta	81.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	41.890 Å
R factor r_factor	0.2430
R_work r_work	0.1990
R_free r_free	0.2480

Crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase

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

Bifunctional purine biosynthesis protein PURH

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

2b1g__assembly_1__model_1

2b1g__assembly_1__model_1 | I(q)

2b1g__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) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. Citations (8)

Crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase

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

Bifunctional purine biosynthesis protein PURH

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

2b1g__assembly_1__model_1

2b1g__assembly_1__model_1 | I(q)

2b1g__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) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. Citations (8)