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1ocp

SOLUTION STRUCTURE OF OCT3 POU-HOMEODOMAIN

Method: SOLUTION NMR Dmax: 40.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

OCT-3

Mus musculus

UniProt P20263

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 217–282 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 1OCP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3L1P POU protein:DNA complex Deposited 2009-12-14 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 131–282（152 aa） Fragment：UNP residues 131-282
Chain B 131–282（152 aa） Fragment：UNP residues 131-282
Mutation：C48S, C61S, C84S, C115S, C142S Mutation：C48S, C61S, C84S, C115S, C142S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.80 Å R-free 0.257
6HT5 Oct4/Sox2:UTF1 structure Deposited 2018-10-03 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 E 131–282（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM 4-morpholineethanesulfonic acid at pH 6.0, 33% v/v 2-methyl-2,4-pentanediol
Resolution 3.45 Å R-free 0.248
8BX1 Oct4/Sox2 protein:DNA complex Deposited 2022-12-07 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 131–282（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M sodium acetate, 12% (v/v) PEG 4000
Resolution 2.50 Å R-free 0.274
8BX2 Oct4/Sox2 protein:DNA complex Deposited 2022-12-07 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 131–282（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M HEPES, 70% (v/v) MPD
Resolution 3.14 Å R-free 0.252

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

View Construct and Data Evidence
UniProt name PO5F1_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–67； UniProt 217–282

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 1ocp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ocp
Deposition date deposition_date1995-02-21
Structure title titleSOLUTION STRUCTURE OF OCT3 POU-HOMEODOMAIN
Keywords keywordsDNA-BINDING PROTEIN, DNA 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_guinier15.15 Å
Radius of gyration Rg (electron density) rg_electron14.39 Å
Forward intensity I(0) i0387290000.00
Molecular weight molecular_weight160470.0 kDa
Excluded volume excluded_volume200690 ų
Envelope volume envelope_volume64193 ų
Hydration-shell volume shell_volume25300 ų
Envelope diameter envelope_diameter70.5 Å
Shell Rg shell_rg28.07 Å
Envelope Rg envelope_rg20.88 Å
Shape Rg shape_rg14.27 Å
Total Rg total_rg15.40 Å
Total atoms total_atoms23140
Residues n_residues1340
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 dmax40.9 Å
Rg (real space) rg_real14.31 Å
Rg uncertainty (real space) rg_real_error0.04 Å
I(0) (real space) i0_real3.6820e+08
I(0) uncertainty (real space) i0_real_error2.5140e+06
Rg (reciprocal space) rg_reciprocal15.23 Å
I(0) (reciprocal space) i0_reciprocal387300000.0000
Solution quality estimate total_estimate0.6749
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.1 Å
Skewness Skewness skewness0.358
Kurtosis Kurtosis kurtosis-0.308
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha3.4750
Highest regularization parameter α highest_alpha9722000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.005; Oscil: 0.949; Stabil: 0.977; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ocpa_
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

CATH v4.4 (1 domains)

Domain ID domain_id1ocpA00
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 (2)

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9. Files and Curves (10)