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1by1

DBL homology domain from beta-PIX

Method: SOLUTION NMR Dmax: 80.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (PIX)

Homo sapiens

UniProt Q14155

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 81–289 Fragment：DBL HOMOLOGY DOMAIN No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；311 K；Ionic strength (raw mmCIF value) 150mM；Pressure 1 NMR sample composition：90% H2O/10% D2O 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 1BY1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ZSG beta PIX-SH3 complexed with an atypical peptide from alpha-PAK Deposited 2005-05-24 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 179–243（65 aa） Fragment：sequence database residues 179-243
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 100 mM Na2SO4；Pressure 1
NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 100 mM Na2SO4；Pressure 1
NMR sample composition 1mM 15N labelled PIX-SH3 complexed with 1.2 mM peptide in 20 mM Na2HPO4/NaH2PO4, pH 7.3, 100mM Na2SO4, 0.05% NaN3, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM 15N,13C labelled PIX-SH3 complexed with 1.2 mM peptide in 20 mM Na2HPO4/NaH2PO4, pH 7.3, 100mM Na2SO4, 0.05% NaN3, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2L3G Solution NMR Structure of CH domain of Rho guanine nucleotide exchange factor 7 from Homo sapiens, Northeast Structural Genomics Consortium Target HR4495E Deposited 2010-09-13 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–137（137 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 0.87 mM [U-100% 13C; U-100% 15N] HR4495E, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.85 mM [U-5% 13C; U-100% 15N] HR4495E, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
5SXP STRUCTURAL BASIS FOR THE INTERACTION BETWEEN ITCH PRR AND BETA-PIX Deposited 2016-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 183–243（61 aa） Fragment：UNP residues 183-243
Chain C 183–243（61 aa） Fragment：UNP residues 183-243
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MIB buffer pH 5.0 and 25% PEG1500
Resolution 1.65 Å R-free 0.161
5SXP STRUCTURAL BASIS FOR THE INTERACTION BETWEEN ITCH PRR AND BETA-PIX Deposited 2016-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 183–243（61 aa） Fragment：UNP residues 183-243
Chain D 183–243（61 aa） Fragment：UNP residues 183-243
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MIB buffer pH 5.0 and 25% PEG1500
Resolution 1.65 Å R-free 0.161

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

View Construct and Data Evidence
UniProt name ARHG7_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–209； UniProt 81–289

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 1by1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1by1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1by1
Deposition date deposition_date1998-10-22
Structure title titleDBL homology domain from beta-PIX
Keywords keywordsRHO-GTPASE EXCHANGE FACTOR, TRANSPORT PROTEIN; TRANSPORT 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_guinier20.66 Å
Radius of gyration Rg (electron density) rg_electron20.31 Å
Forward intensity I(0) i03205080000.00
Molecular weight molecular_weight478830.0 kDa
Excluded volume excluded_volume598850 ų
Envelope volume envelope_volume86739 ų
Hydration-shell volume shell_volume28707 ų
Envelope diameter envelope_diameter89.2 Å
Shell Rg shell_rg32.69 Å
Envelope Rg envelope_rg26.24 Å
Shape Rg shape_rg20.31 Å
Total Rg total_rg20.51 Å
Total atoms total_atoms67220
Residues n_residues4180
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 dmax80.2 Å
Rg (real space) rg_real20.76 Å
Rg uncertainty (real space) rg_real_error0.84 Å
I(0) (real space) i0_real3.2050e+09
I(0) uncertainty (real space) i0_real_error5.0970e+07
Rg (reciprocal space) rg_reciprocal20.74 Å
I(0) (reciprocal space) i0_reciprocal3205000000.0000
Solution quality estimate total_estimate0.7772
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.9 Å
Skewness Skewness skewness0.487
Kurtosis Kurtosis kurtosis-0.159
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3963000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.500; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.617; Smooth: 0.987
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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_idd1by1a1
Class classa — All alpha proteins
Fold Fold folda.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
Family Family familya.87.1.1 — DBL homology domain (DH-domain)
Domain ID domain_idd1by1a2
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_id1by1A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily10 — Dbl homology (DH) domain
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8. Citations (1)

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9. Files and Curves (10)