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1gnd

GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM

Method: X-RAY DIFFRACTION Dmax: 77.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR

Bos taurus

UniProt P21856

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 1–447 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.81 Å R-free 0.275

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 1GND Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D5T GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM Deposited 1999-10-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–431（431 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295.5 K；ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 22.5K
Resolution 1.04 Å R-free 0.209
1LV0 Crystal structure of the Rab effector guanine nucleotide dissociation inhibitor (GDI) in complex with a geranylgeranyl (GG) peptide Deposited 2002-05-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–447（447 aa）
Not recorded SO4 SULFATE ION × 3 GER GERAN-8-YL GERAN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；296 K；Ammonium Sulfate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.00 Å R-free 0.249

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

View Construct and Data Evidence
UniProt name GDIA_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–447； UniProt 1–447

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 1gnd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1gnd
Deposition date deposition_date1996-07-10
Structure title titleGUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM
Keywords keywordsGTPASE ACTIVATION; GTPASE ACTIVATION
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_guinier24.16 Å
Radius of gyration Rg (electron density) rg_electron23.01 Å
Forward intensity I(0) i039203900.00
Molecular weight molecular_weight48496.0 kDa
Excluded volume excluded_volume60826 ų
Envelope volume envelope_volume74223 ų
Hydration-shell volume shell_volume26822 ų
Envelope diameter envelope_diameter81.3 Å
Shell Rg shell_rg30.19 Å
Envelope Rg envelope_rg23.12 Å
Shape Rg shape_rg22.99 Å
Total Rg total_rg23.93 Å
Total atoms total_atoms3405
Residues n_residues430
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 dmax77.9 Å
Rg (real space) rg_real24.07 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real3.9200e+07
I(0) uncertainty (real space) i0_real_error4.6230e+05
Rg (reciprocal space) rg_reciprocal24.09 Å
I(0) (reciprocal space) i0_reciprocal39200000.0000
Solution quality estimate total_estimate0.8982
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.0 Å
Skewness Skewness skewness0.230
Kurtosis Kurtosis kurtosis-0.454
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10970000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985
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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) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1gnda1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.3 — GDI-like N domain
Domain ID domain_idd1gnda2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamilyd.16.1 — FAD-linked reductases, C-terminal domain
Family Family familyd.16.1.6 — GDI-like

CATH v4.4 (3 domains)

Domain ID domain_id1gndA01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1gndA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
Homologous superfamily homologous superfamily10 — Guanine Nucleotide Dissociation Inhibitor, domain 2
Domain ID domain_id1gndA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
Homologous superfamily homologous superfamily10 — Guanine Nucleotide Dissociation Inhibitor, domain 1
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8. Citations (2)

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9. Files and Curves (10)