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1dch

CRYSTAL STRUCTURE OF DCOH, A BIFUNCTIONAL, PROTEIN-BINDING TRANSCRIPTION COACTIVATOR

Method: X-RAY DIFFRACTION Dmax: 114.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DCOH (DIMERIZATION COFACTOR OF HNF-1)

Rattus norvegicus

UniProt P61459

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–103 Chain B； UniProt 1–103 Chain C； UniProt 1–103 Chain D； UniProt 1–103 Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；pH 7.2 COMPND ROOM TEMP., 1.7M AMSO4, .1M HEPES, PH 7.2. Resolution 3.00 Å
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain E； UniProt 1–103 Chain F； UniProt 1–103 Chain G； UniProt 1–103 Chain H； UniProt 1–103 Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；pH 7.2 COMPND ROOM TEMP., 1.7M AMSO4, .1M HEPES, PH 7.2. Resolution 3.00 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 1DCH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DCO DCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR Deposited 1996-05-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–103（103 aa）
Chain B 1–103（103 aa）
Chain C 1–103（103 aa）
Chain D 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；ROOM TEMPERATURE, 1.7M AMSO4, 0.1M HEPES, PH 7.4
Resolution 2.30 Å
1DCO DCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR Deposited 1996-05-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–103（103 aa）
Chain F 1–103（103 aa）
Chain G 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；ROOM TEMPERATURE, 1.7M AMSO4, 0.1M HEPES, PH 7.4
Resolution 2.30 Å
1DCP DCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR, COMPLEXED WITH BIOPTERIN Deposited 1996-05-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–103（103 aa）
Chain B 1–103（103 aa）
Chain C 1–103（103 aa）
Chain D 1–103（103 aa）
Not recorded HBI 7,8-DIHYDROBIOPTERIN × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；ROOM TEMPERATURE, 1.7M AMSO4, 0.1M HEPES, PH 7.4
Resolution 2.30 Å
1DCP DCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR, COMPLEXED WITH BIOPTERIN Deposited 1996-05-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–103（103 aa）
Chain F 1–103（103 aa）
Chain G 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded HBI 7,8-DIHYDROBIOPTERIN × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；ROOM TEMPERATURE, 1.7M AMSO4, 0.1M HEPES, PH 7.4
Resolution 2.30 Å
1F93 CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE DIMERIZATION DOMAIN OF HNF-1 ALPHA AND THE COACTIVATOR DCOH Deposited 2000-07-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–104（104 aa）
Chain B 1–104（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；PEG 8000, potassium succinate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.60 Å R-free 0.299
1F93 CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE DIMERIZATION DOMAIN OF HNF-1 ALPHA AND THE COACTIVATOR DCOH Deposited 2000-07-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–104（104 aa）
Chain D 1–104（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；PEG 8000, potassium succinate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.60 Å R-free 0.299
3HXA Crystal Structure of DCoH1Thr51Ser Deposited 2009-06-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–104（104 aa）
Chain B 1–104（104 aa）
Chain C 1–104（104 aa）
Chain D 1–104（104 aa）
Mutation：T51S Mutation：T51S Mutation：T51S Mutation：T51S SO4 SULFATE ION × 4 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions Hanging drop；pH 7.5；291 K；HEPES, Ammonium Sulfate, PEG 200, Glycerol, pH 7.5, Hanging drop, temperature 291K
Resolution 1.80 Å R-free 0.226
3HXA Crystal Structure of DCoH1Thr51Ser Deposited 2009-06-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–104（104 aa）
Chain F 1–104（104 aa）
Chain G 1–104（104 aa）
Chain H 1–104（104 aa）
Mutation：T51S Mutation：T51S Mutation：T51S Mutation：T51S SO4 SULFATE ION × 4 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions Hanging drop；pH 7.5；291 K；HEPES, Ammonium Sulfate, PEG 200, Glycerol, pH 7.5, Hanging drop, temperature 291K
Resolution 1.80 Å R-free 0.226

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

View Construct and Data Evidence
UniProt name PHS_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–104； UniProt 1–103 Author chain B； PDBConstruct 2–104； UniProt 1–103 Author chain C； PDBConstruct 2–104； UniProt 1–103 Author chain D； PDBConstruct 2–104； UniProt 1–103 Author chain E； PDBConstruct 2–104； UniProt 1–103 Author chain F； PDBConstruct 2–104； UniProt 1–103 Author chain G； PDBConstruct 2–104； UniProt 1–103 Author chain H； PDBConstruct 2–104； UniProt 1–103

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 1dch

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1dch
Deposition date deposition_date1995-01-24
Structure title titleCRYSTAL STRUCTURE OF DCOH, A BIFUNCTIONAL, PROTEIN-BINDING TRANSCRIPTION COACTIVATOR
Keywords keywords;TRANSCRIPTIONAL SIMULATOR, DIMERIZATION COFACTOR, DEHYDRATASE, 4A-CARBINOLAMINE DEHYDRATASE, TRANSREGULATOR OF HOMEODOMAIN PROTEINS, TRANSCRIPTIONAL STIMULATOR, DIMERIZATION ;; TRANSCRIPTIONAL STIMULATOR,DIMERIZATION
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_guinier35.50 Å
Radius of gyration Rg (electron density) rg_electron34.87 Å
Forward intensity I(0) i0137497000.00
Molecular weight molecular_weight92022.0 kDa
Excluded volume excluded_volume114080 ų
Envelope volume envelope_volume146290 ų
Hydration-shell volume shell_volume35990 ų
Envelope diameter envelope_diameter116.4 Å
Shell Rg shell_rg40.02 Å
Envelope Rg envelope_rg34.57 Å
Shape Rg shape_rg34.84 Å
Total Rg total_rg35.30 Å
Total atoms total_atoms6494
Residues n_residues792
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 dmax114.5 Å
Rg (real space) rg_real35.58 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real1.3750e+08
I(0) uncertainty (real space) i0_real_error2.1540e+06
Rg (reciprocal space) rg_reciprocal35.54 Å
I(0) (reciprocal space) i0_reciprocal137500000.0000
Solution quality estimate total_estimate0.8945
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.6 Å
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.712
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11260000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.939
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1dcha_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.1 — PCD-like
Family Family familyd.74.1.1 — PCD-like
Domain ID domain_idd1dchb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.1 — PCD-like
Family Family familyd.74.1.1 — PCD-like
Domain ID domain_idd1dchc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.1 — PCD-like
Family Family familyd.74.1.1 — PCD-like
Domain ID domain_idd1dchd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.1 — PCD-like
Family Family familyd.74.1.1 — PCD-like
Domain ID domain_idd1dche_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.1 — PCD-like
Family Family familyd.74.1.1 — PCD-like
Domain ID domain_idd1dchf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.1 — PCD-like
Family Family familyd.74.1.1 — PCD-like
Domain ID domain_idd1dchg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.1 — PCD-like
Family Family familyd.74.1.1 — PCD-like
Domain ID domain_idd1dchh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.74 — DCoH-like
Superfamily Superfamily superfamilyd.74.1 — PCD-like
Family Family familyd.74.1.1 — PCD-like

CATH v4.4 (8 domains)

Domain ID domain_id1dchA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily20 — Transcriptional coactivator/pterin dehydratase
Domain ID domain_id1dchB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily20 — Transcriptional coactivator/pterin dehydratase
Domain ID domain_id1dchC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily20 — Transcriptional coactivator/pterin dehydratase
Domain ID domain_id1dchD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily20 — Transcriptional coactivator/pterin dehydratase
Domain ID domain_id1dchE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily20 — Transcriptional coactivator/pterin dehydratase
Domain ID domain_id1dchF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily20 — Transcriptional coactivator/pterin dehydratase
Domain ID domain_id1dchG00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily20 — Transcriptional coactivator/pterin dehydratase
Domain ID domain_id1dchH00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily20 — Transcriptional coactivator/pterin dehydratase
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8. Citations (1)

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9. Files and Curves (10)