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1pog

SOLUTION STRUCTURE OF THE OCT-1 POU-HOMEO DOMAIN DETERMINED BY NMR AND RESTRAINED MOLECULAR DYNAMICS

Method: SOLUTION NMR Dmax: 53.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

OCT-1 POU HOMEODOMAIN DNA-BINDING PROTEIN

Homo sapiens

UniProt P14859

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 378–437 Not recorded No other associated polymer SOLUTION NMR mmCIF provides none of the parsed experimental conditions Resolution not provided

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 1POG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CQT CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTIDE, THE OCT-1 POU DOMAIN, AND AN OCTAMER ELEMENT Deposited 1999-08-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 277–439（163 aa） Fragment：OCT-1 POU DOMAIN, RESIDUES 278-439
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.326
1CQT CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTIDE, THE OCT-1 POU DOMAIN, AND AN OCTAMER ELEMENT Deposited 1999-08-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 277–439（163 aa） Fragment：OCT-1 POU DOMAIN, RESIDUES 278-439
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.326
1E3O Crystal structure of Oct-1 POU dimer bound to MORE Deposited 2000-06-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain C 280–438（159 aa） Fragment：DNA-BINDING DOMAIN
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；22% PEG3350, 50MM HEPES, PH 7.0, 1.8MM SPERMINE
Resolution 1.90 Å R-free 0.242
1GT0 Crystal structure of a POU/HMG/DNA ternary complex Deposited 2002-01-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain C 280–438（159 aa） Fragment：POU DOMAIN RESIDUES 280-438
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；18% PEG3350, 50 MM HEPES PH 7.0, 20 MM MGCL2, 5% GLYCEROL
Resolution 2.60 Å R-free 0.285
1HF0 Crystal structure of the DNA-binding domain of Oct-1 bound to DNA as a dimer Deposited 2000-11-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 280–438（159 aa） Fragment：DNA-BINDING DOMAIN
Chain B 280–438（159 aa） Fragment：DNA-BINDING DOMAIN
Mutation：YES Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；pH 5.30
Resolution 2.70 Å R-free 0.294
1O4X TERNARY COMPLEX OF THE DNA BINDING DOMAINS OF THE OCT1 AND SOX2 TRANSCRIPTION FACTORS WITH A 19MER OLIGONUCLEOTIDE FROM THE HOXB1 REGULATORY ELEMENT Deposited 2003-07-17 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 303–465（163 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 10 mM SODIUM PHOSPHATE
Resolution not provided
1OCT CRYSTAL STRUCTURE OF THE OCT-1 POU DOMAIN BOUND TO AN OCTAMER SITE: DNA RECOGNITION WITH TETHERED DNA-BINDING MODULES Deposited 1994-05-09 Different construct Different oligomeric state Different experimental method Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 284–439（156 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1POU THE SOLUTION STRUCTURE OF THE OCT-1 POU-SPECIFIC DOMAIN REVEALS A STRIKING SIMILARITY TO THE BACTERIOPHAGE LAMBDA REPRESSOR DNA-BINDING DOMAIN Deposited 1993-06-14 Different construct Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 284–354（71 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided

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

View Construct and Data Evidence
UniProt name PO2F1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–65； UniProt 378–437

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 1pog

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1pog
Deposition date deposition_date1994-10-12
Structure title titleSOLUTION STRUCTURE OF THE OCT-1 POU-HOMEO DOMAIN DETERMINED BY NMR AND RESTRAINED MOLECULAR DYNAMICS
Keywords keywordsDNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.37 Å
Radius of gyration Rg (electron density) rg_electron12.02 Å
Forward intensity I(0) i0149079000.00
Molecular weight molecular_weight98942.0 kDa
Excluded volume excluded_volume123370 ų
Envelope volume envelope_volume22677 ų
Hydration-shell volume shell_volume13010 ų
Envelope diameter envelope_diameter54.9 Å
Shell Rg shell_rg20.75 Å
Envelope Rg envelope_rg15.49 Å
Shape Rg shape_rg11.96 Å
Total Rg total_rg12.56 Å
Total atoms total_atoms14130
Residues n_residues806
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 dmax53.1 Å
Rg (real space) rg_real12.38 Å
Rg uncertainty (real space) rg_real_error0.62 Å
I(0) (real space) i0_real1.4910e+08
I(0) uncertainty (real space) i0_real_error2.0110e+06
Rg (reciprocal space) rg_reciprocal12.37 Å
I(0) (reciprocal space) i0_reciprocal149100000.0000
Solution quality estimate total_estimate0.7122
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary14.8 Å
Skewness Skewness skewness0.422
Kurtosis Kurtosis kurtosis0.282
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha230500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.235; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.550; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1poga1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.1 — Homeodomain-like
Family Family familya.4.1.1 — Homeodomain
Domain ID domain_idd1poga2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1pogA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
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8. Citations (1)

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9. Files and Curves (10)