SAXSdb — 1jkx

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

PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–212 Chain B； UniProt 1–212	Fragment：TRANSFERASE	138 N-[5'-O-PHOSPHONO-RIBOFURANOSYL]-2-[2-HYDROXY-2-[4-[GLUTAMIC ACID]-N-CARBONYLPHENYL]-3-[2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL]-PROPANYLAMINO]-ACETAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；PEG 3350, CaCl2, MPD, imidazole malate, PH 7.4, VAPOR DIFFUSION, SITTING DROP at 295K	Resolution 1.60 Å R-free 0.243
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–212 Chain D； UniProt 1–212	Fragment：TRANSFERASE	138 N-[5'-O-PHOSPHONO-RIBOFURANOSYL]-2-[2-HYDROXY-2-[4-[GLUTAMIC ACID]-N-CARBONYLPHENYL]-3-[2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL]-PROPANYLAMINO]-ACETAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；PEG 3350, CaCl2, MPD, imidazole malate, PH 7.4, VAPOR DIFFUSION, SITTING DROP at 295K	Resolution 1.60 Å R-free 0.243

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1JKX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C2T NEW INSIGHTS INTO INHIBITOR DESIGN FROM THE CRYSTAL STRUCTURE AND NMR STUDIES OF E. COLI GAR TRANSFORMYLASE IN COMPLEX WITH BETA-GAR AND 10-FORMYL-5,8,10-TRIDEAZAFOLIC ACID. Deposited 1999-07-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–212（212 aa） Chain B 1–212（212 aa）	Not recorded	NHS 10-FORMYL-5,8,10-TRIDEAZAFOLIC ACID × 2 GAR GLYCINAMIDE RIBONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；295 K；PEG 3350, IMIDAZOLE MALATE, CALCIUM CHLORIDE, MPD, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 22.0K, temperature 295K	Resolution 2.10 Å R-free 0.265
1C3E NEW INSIGHTS INTO INHIBITOR DESIGN FROM THE CRYSTAL STRUCTURE AND NMR STUDIES OF E. COLI GAR TRANSFORMYLATE IN COMPLEX WITH BETA-GAR AND 10-FORMYL-5,8,10-TRIDEAZAFOLIC ACID. Deposited 1999-07-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain not uniquely mapped Reference range not declared Chain A 1–209（209 aa）	Not recorded	NHR 2-{4-[2-(2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL)-1-CARBOXY-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID × 2 GAR GLYCINAMIDE RIBONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；295 K；PEG 3350, Imidazole malate, calcium chloride, MPD, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 22.0K	Resolution 2.10 Å R-free 0.263
1CDD STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE Deposited 1992-05-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–212（212 aa） Chain B 1–212（212 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1CDD STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE Deposited 1992-05-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–212（212 aa） Chain B 1–212（212 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1CDE STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE Deposited 1992-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–212（212 aa）	Not recorded	GAR GLYCINAMIDE RIBONUCLEOTIDE × 1 DZF 5-DEAZAFOLIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1CDE STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE Deposited 1992-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–212（212 aa）	Not recorded	GAR GLYCINAMIDE RIBONUCLEOTIDE × 1 DZF 5-DEAZAFOLIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1CDE STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE Deposited 1992-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–212（212 aa）	Not recorded	GAR GLYCINAMIDE RIBONUCLEOTIDE × 1 DZF 5-DEAZAFOLIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1CDE STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE Deposited 1992-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–212（212 aa）	Not recorded	GAR GLYCINAMIDE RIBONUCLEOTIDE × 1 DZF 5-DEAZAFOLIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1GAR TOWARDS STRUCTURE-BASED DRUG DESIGN: CRYSTAL STRUCTURE OF A MULTISUBSTRATE ADDUCT COMPLEX OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE AT 1.96 ANGSTROMS RESOLUTION Deposited 1994-12-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–212（212 aa） Chain B 1–212（212 aa）	Not recorded	U89 N-[4-[[3-(2,4-DIAMINO-1,6-DIHYDRO-6-OXO-4-PYRIMIDINYL)-PROPYL]-[2-((2-OXO-2-((4-PHOSPHORIBOXY)-BUTYL)-AMINO)-ETHYL)-THIO-ACETYL]-AMINO]BENZOYL]-1-GLUTAMIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.96 Å R-free 0.290
1GRC CRYSTAL STRUCTURE OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE FROM ESCHERICHIA COLI AT 3.0 ANGSTROMS RESOLUTION: A TARGET ENZYME FOR CHEMOTHERAPY Deposited 1992-07-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–212（212 aa） Chain B 1–212（212 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2GAR A PH-DEPENDENT STABLIZATION OF AN ACTIVE SITE LOOP OBSERVED FROM LOW AND HIGH PH CRYSTAL STRUCTURES OF MUTANT MONOMERIC GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE Deposited 1998-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–212（212 aa）	Mutation：E70A	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.5；CRYSTAL GREW FROM A SOLUTION OF 2%(V/V) 15% (W/V) PEG 1500, PH 3.5	Resolution 1.80 Å R-free 0.251
3GAR A PH-DEPENDENT STABLIZATION OF AN ACTIVE SITE LOOP OBSERVED FROM LOW AND HIGH PH CRYSTAL STRUCTURES OF MUTANT MONOMERIC GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE Deposited 1998-05-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–212（212 aa）	Mutation：E70A	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；CRYSTAL GREW FROM A SOLUTION OF 2%(V/V) PEG 400. 2.0M AMMONIUM SULFATE, 0.1M HEPES, PH 7.5	Resolution 1.90 Å R-free 0.274

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PUR3_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–212； UniProt 1–212 Author chain B； PDBConstruct 1–212； UniProt 1–212 Author chain C； PDBConstruct 1–212； UniProt 1–212 Author chain D； 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	1jkx
Deposition date deposition_date	2001-07-13
Structure title title	Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase
Keywords keywords	PURINE BIOSYNTHESIS, ANTI-CANCER AGENT, ENZYME-ASSEMBLED MULTISUBSTRATE ADDUCT INHIBITOR COMPLEX, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.12 Å
Radius of gyration Rg (electron density) rg_electron	35.42 Å
Forward intensity I(0) i0	142525000.00
Molecular weight molecular_weight	94607.0 kDa
Excluded volume excluded_volume	117840 Å³
Envelope volume envelope_volume	160040 Å³
Hydration-shell volume shell_volume	38971 Å³
Envelope diameter envelope_diameter	116.8 Å
Shell Rg shell_rg	40.72 Å
Envelope Rg envelope_rg	34.55 Å
Shape Rg shape_rg	35.43 Å
Total Rg total_rg	35.74 Å
Total atoms total_atoms	6676
Residues n_residues	836
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	114.8 Å
Rg (real space) rg_real	36.00 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	1.4250e+08
I(0) uncertainty (real space) i0_real_error	2.4240e+06
Rg (reciprocal space) rg_reciprocal	36.08 Å
I(0) (reciprocal space) i0_reciprocal	142500000.0000
Solution quality estimate total_estimate	0.8986
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	52.2 Å
Skewness Skewness skewness	0.079
Kurtosis Kurtosis kurtosis	-0.676
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18070000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.940

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
Molecular weight formula_weight	23266.3 kDa
EC 编号 ec_number	2.1.2.2
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	7283

MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYAADE

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;N-[5'-O-PHOSPHONO-RIBOFURANOSYL]-2-[2-HYDROXY-2-[4-[GLUTAMIC ACID]-N-CARBONYLPHENYL]-3-[2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL]-PROPANYLAMINO]-ACETAMIDE ;
Molecular weight formula_weight	752.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	607

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1jkxa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.65 — Formyltransferase
Superfamily Superfamily superfamily	c.65.1 — Formyltransferase
Family Family family	c.65.1.1 — Formyltransferase

Domain ID domain_id	d1jkxb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.65 — Formyltransferase
Superfamily Superfamily superfamily	c.65.1 — Formyltransferase
Family Family family	c.65.1.1 — Formyltransferase

Domain ID domain_id	d1jkxc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.65 — Formyltransferase
Superfamily Superfamily superfamily	c.65.1 — Formyltransferase
Family Family family	c.65.1.1 — Formyltransferase

Domain ID domain_id	d1jkxd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.65 — Formyltransferase
Superfamily Superfamily superfamily	c.65.1 — Formyltransferase
Family Family family	c.65.1.1 — Formyltransferase

CATH v4.4 (4 domains)

Domain ID domain_id	1jkxA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	170 — Formyl transferase, N-terminal domain

Domain ID domain_id	1jkxB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	170 — Formyl transferase, N-terminal domain

Domain ID domain_id	1jkxC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	170 — Formyl transferase, N-terminal domain

Domain ID domain_id	1jkxD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	170 — Formyl transferase, N-terminal domain

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8. Citations (2)

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Unit-cell length a length_a	55.140 Å
Unit-cell length b length_b	56.010 Å
Unit-cell length c length_c	76.130 Å
Unit-cell angle α angle_alpha	80.83 °
Unit-cell angle β angle_beta	71.71 °
Unit-cell angle γ angle_gamma	83.69 °
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	1.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2210
R_work r_work	0.2210
R_free r_free	0.2430

fit	/app/data/saxs_computation/jk/1jkx/1jkx.fit
pddf	/app/data/pr_computation/jk/1jkx/1jkx.pr.out
profile	/app/data/saxs_computation/jk/1jkx/1jkx.dat

Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase

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

PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction