1lfd

CRYSTAL STRUCTURE OF THE ACTIVE RAS PROTEIN COMPLEXED WITH THE RAS-INTERACTING DOMAIN OF RALGDS

Method: X-RAY DIFFRACTION Dmax: 79.4 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

RALGDS

Rattus norvegicus

UniProt Q03386

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 778–864 Fragment:RAS-INTERACTING DOMAIN, C-TERMINAL DOMAIN RAS × 1 (P01112) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 2.10 Å R-free 0.282
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 778–864 Fragment:RAS-INTERACTING DOMAIN, C-TERMINAL DOMAIN RAS × 1 (P01112) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 2.10 Å R-free 0.282

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNDS_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–87; UniProt 778–864 Author chain C; PDBConstruct 1–87; UniProt 778–864

RAS

Homo sapiens

UniProt P01112

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–167 Fragment:RESIDUES 1-171 Mutation:E31K RALGDS × 1 (Q03386) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 2.10 Å R-free 0.282
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–167 Fragment:RESIDUES 1-171 Mutation:E31K RALGDS × 1 (Q03386) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 2.10 Å R-free 0.282

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.

242 other PDB entries and 323 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RASH_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–167; UniProt 1–167 Author chain D; PDBConstruct 1–167; UniProt 1–167

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 1lfd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1lfd
Deposition date deposition_date1998-04-29
Structure title titleCRYSTAL STRUCTURE OF THE ACTIVE RAS PROTEIN COMPLEXED WITH THE RAS-INTERACTING DOMAIN OF RALGDS
Keywords keywordsCOMPLEX (RALGDS-RAS), RAL, EFFECTOR INTERACTION, COMPLEX (RALGDS-RAS) complex; COMPLEX (RALGDS/RAS)
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.43
Radius of gyration Rg (electron density) rg_electron23.45
Forward intensity I(0) i062173000.00
Molecular weight molecular_weight58918.0 kDa
Excluded volume excluded_volume72732 ų
Envelope volume envelope_volume86500 ų
Hydration-shell volume shell_volume30077 ų
Envelope diameter envelope_diameter80.9
Shell Rg shell_rg31.21
Envelope Rg envelope_rg23.54
Shape Rg shape_rg23.47
Total Rg total_rg24.24
Total atoms total_atoms4122
Residues n_residues508
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax79.4
Rg (real space) rg_real24.30
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real6.2170e+07
I(0) uncertainty (real space) i0_real_error8.7970e+05
Rg (reciprocal space) rg_reciprocal24.33
I(0) (reciprocal space) i0_reciprocal62170000.0000
Solution quality estimate total_estimate0.8869
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.0
Skewness Skewness skewness0.221
Kurtosis Kurtosis kurtosis-0.351
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16890000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.981

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1lfda_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.5 — Ras-binding domain, RBD
Domain ID domain_idd1lfdb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd1lfdc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.5 — Ras-binding domain, RBD
Domain ID domain_idd1lfdd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins

CATH v4.4 (4 domains)

Domain ID domain_id1lfdA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id1lfdB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1lfdC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id1lfdD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (4)

9. Files and Curves (10)