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1tkb

SPECIFICITY OF COENZYME BINDING IN THIAMIN DIPHOSPHATE DEPENDENT ENZYMES: CRYSTAL STRUCTURES OF YEAST TRANSKETOLASE IN COMPLEX WITH ANALOGS OF THIAMIN DIPHOSPHATE

Method: X-RAY DIFFRACTION Dmax: 93.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TRANSKETOLASE

Saccharomyces cerevisiae

UniProt P23254

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 2–679 Chain B； UniProt 2–679 Not recorded CA CALCIUM ION × 2 N1T 1'-DEAZO-THIAMIN DIPHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.30 Å

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 1TKB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AY0 IDENTIFICATION OF CATALYTICALLY IMPORTANT RESIDUES IN YEAST TRANSKETOLASE Deposited 1997-11-13 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 1–679（679 aa）
Chain B 1–679（679 aa）
Mutation：H263A Mutation：H263A CA CALCIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；SEE PAPER SCHNEIDER ET AL., (1989), J. BIOL. CHEM. 264,21619-21620, pH 7.5
Resolution 2.60 Å R-free 0.263
1GPU Transketolase complex with reaction intermediate Deposited 2001-11-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–680（680 aa）
Chain B 1–680（680 aa）
Not recorded CA CALCIUM ION × 2 THD 2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.9；pH 7.90
Resolution 1.86 Å R-free 0.225
1NGS COMPLEX OF TRANSKETOLASE WITH THIAMIN DIPHOSPHATE, CA2+ AND ACCEPTOR SUBSTRATE ERYTHROSE-4-PHOSPHATE Deposited 1996-09-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–679（679 aa）
Chain B 1–679（679 aa）
Not recorded CA CALCIUM ION × 2 E4P ERYTHOSE-4-PHOSPHATE × 2 TPP THIAMINE DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；SEE THE PAPER, pH 7.6
Resolution 2.40 Å R-free 0.239
1TKA SPECIFICITY OF COENZYME BINDING IN THIAMIN DIPHOSPHATE DEPENDENT ENZYMES: CRYSTAL STRUCTURES OF YEAST TRANSKETOLASE IN COMPLEX WITH ANALOGS OF THIAMIN DIPHOSPHATE Deposited 1994-02-07 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–679（678 aa）
Chain B 2–679（678 aa）
Not recorded CA CALCIUM ION × 2 N3T 3'-DEAZO-THIAMIN DIPHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1TKC SPECIFICITY OF COENZYME BINDING IN THIAMIN DIPHOSPHATE DEPENDENT ENZYMES: CRYSTAL STRUCTURES OF YEAST TRANSKETOLASE IN COMPLEX WITH ANALOGS OF THIAMIN DIPHOSPHATE Deposited 1994-02-07 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–679（678 aa）
Chain B 2–679（678 aa）
Not recorded CA CALCIUM ION × 2 M6T 6'-METHYL-THIAMIN DIPHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1TRK REFINED STRUCTURE OF TRANSKETOLASE FROM SACCHAROMYCES CEREVISIAE AT 2.0 ANGSTROMS RESOLUTION Deposited 1993-11-22 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–679（679 aa）
Chain B 1–679（679 aa）
Not recorded CA CALCIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TKT1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–678； UniProt 2–679 Author chain B； PDBConstruct 1–678； UniProt 2–679

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1tkb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1tkb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1tkb
Deposition date deposition_date1994-02-07
Structure title titleSPECIFICITY OF COENZYME BINDING IN THIAMIN DIPHOSPHATE DEPENDENT ENZYMES: CRYSTAL STRUCTURES OF YEAST TRANSKETOLASE IN COMPLEX WITH ANALOGS OF THIAMIN DIPHOSPHATE
Keywords keywordsTRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.10 Å
Radius of gyration Rg (electron density) rg_electron31.35 Å
Forward intensity I(0) i0330777000.00
Molecular weight molecular_weight148070.0 kDa
Excluded volume excluded_volume185890 ų
Envelope volume envelope_volume215250 ų
Hydration-shell volume shell_volume54001 ų
Envelope diameter envelope_diameter102.3 Å
Shell Rg shell_rg40.64 Å
Envelope Rg envelope_rg31.66 Å
Shape Rg shape_rg31.34 Å
Total Rg total_rg32.08 Å
Total atoms total_atoms10450
Residues n_residues1356
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax93.1 Å
Rg (real space) rg_real31.86 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real3.3080e+08
I(0) uncertainty (real space) i0_real_error4.6870e+06
Rg (reciprocal space) rg_reciprocal31.96 Å
I(0) (reciprocal space) i0_reciprocal330800000.0000
Solution quality estimate total_estimate0.9061
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.8 Å
Skewness Skewness skewness0.098
Kurtosis Kurtosis kurtosis-0.548
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha148700000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.882
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1tkba1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.10 — TK-like PP module
Domain ID domain_idd1tkba2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.6 — TK-like Pyr module
Domain ID domain_idd1tkba3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.48 — TK C-terminal domain-like
Superfamily Superfamily superfamilyc.48.1 — TK C-terminal domain-like
Family Family familyc.48.1.1 — Transketolase C-terminal domain-like
Domain ID domain_idd1tkbb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.10 — TK-like PP module
Domain ID domain_idd1tkbb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.6 — TK-like Pyr module
Domain ID domain_idd1tkbb3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.48 — TK C-terminal domain-like
Superfamily Superfamily superfamilyc.48.1 — TK C-terminal domain-like
Family Family familyc.48.1.1 — Transketolase C-terminal domain-like

CATH v4.4 (6 domains)

Domain ID domain_id1tkbA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1tkbA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1tkbA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id1tkbB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1tkbB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1tkbB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
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8. Citations (5)

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9. Files and Curves (10)