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1upr

Crystal structure of the PEPP1 pleckstrin homology domain in complex with Inositol 1,3,4,5-tetrakisphosphate

Method: X-RAY DIFFRACTION Dmax: 46.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY A MEMBER 4

HOMO SAPIENS

UniProt Q9H4M7

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 45–167 Fragment：PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 45-167 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；16% PEG 20,000, 0.1 M MES (PH 6.0) Resolution 2.27 Å R-free 0.276

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 1UPR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1UPQ Crystal structure of the pleckstrin homology (PH) domain of PEPP1 Deposited 2003-10-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 45–167（123 aa） Fragment：PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 45-167
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；25% PEG 5000 MME, 0.2 M AMMONIUM SULFATE, 0.1 M MES PH 6.5
Resolution 1.48 Å R-free 0.243
8OIO Crystal structure of the kelch domain of human KLHL12 in complex with PLEKHA4 peptide Deposited 2023-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 174–184（11 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1 M citrate pH 5.5, 0.4 M NaCl, 27,1% PEG8K
Resolution 1.95 Å R-free 0.249
8OIO Crystal structure of the kelch domain of human KLHL12 in complex with PLEKHA4 peptide Deposited 2023-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 174–184（11 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1 M citrate pH 5.5, 0.4 M NaCl, 27,1% PEG8K
Resolution 1.95 Å R-free 0.249
8OIO Crystal structure of the kelch domain of human KLHL12 in complex with PLEKHA4 peptide Deposited 2023-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 174–184（11 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1 M citrate pH 5.5, 0.4 M NaCl, 27,1% PEG8K
Resolution 1.95 Å R-free 0.249
8OIO Crystal structure of the kelch domain of human KLHL12 in complex with PLEKHA4 peptide Deposited 2023-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 174–184（11 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1 M citrate pH 5.5, 0.4 M NaCl, 27,1% PEG8K
Resolution 1.95 Å R-free 0.249

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PKHA4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–123； UniProt 45–167

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 1upr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1upr
Deposition date deposition_date2003-10-10
Structure title titleCrystal structure of the PEPP1 pleckstrin homology domain in complex with Inositol 1,3,4,5-tetrakisphosphate
Keywords keywordsSIGNALING PROTEIN, SIGNAL TRANSDUCTION, PHOSPHOINOSITIDE BINDING DOMAIN; SIGNALING PROTEIN
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_guinier14.90 Å
Radius of gyration Rg (electron density) rg_electron13.40 Å
Forward intensity I(0) i03788150.00
Molecular weight molecular_weight12923.0 kDa
Excluded volume excluded_volume15896 ų
Envelope volume envelope_volume18235 ų
Hydration-shell volume shell_volume11593 ų
Envelope diameter envelope_diameter45.5 Å
Shell Rg shell_rg19.16 Å
Envelope Rg envelope_rg13.73 Å
Shape Rg shape_rg13.35 Å
Total Rg total_rg14.77 Å
Total atoms total_atoms908
Residues n_residues107
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 dmax46.9 Å
Rg (real space) rg_real14.78 Å
Rg uncertainty (real space) rg_real_error0.21 Å
I(0) (real space) i0_real3.7880e+06
I(0) uncertainty (real space) i0_real_error3.9560e+04
Rg (reciprocal space) rg_reciprocal14.79 Å
I(0) (reciprocal space) i0_reciprocal3788000.0000
Solution quality estimate total_estimate0.8872
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.3 Å
Skewness Skewness skewness0.052
Kurtosis Kurtosis kurtosis-0.371
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha669900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.985
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1upra_
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.1 — Pleckstrin-homology domain (PH domain)

CATH v4.4 (1 domains)

Domain ID domain_id1uprA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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8. Citations (1)

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9. Files and Curves (10)