SAXSdb — 4iru

▼

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

LepB

Legionella pneumophila

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 326–623	Fragment：LepB GAP domain, catalytic core Non-standard monomer：Yes (specific site not provided by mmCIF)	Ras-related protein Rab-1A × 1 （P62820） ACT ACETATE ION × 4 GOL GLYCEROL × 7 K POTASSIUM ION × 5 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.288
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 326–623	Fragment：LepB GAP domain, catalytic core Non-standard monomer：Yes (specific site not provided by mmCIF)	Ras-related protein Rab-1A × 1 （P62820） ACT ACETATE ION × 8 GOL GLYCEROL × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.288
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 326–623	Fragment：LepB GAP domain, catalytic core Non-standard monomer：Yes (specific site not provided by mmCIF)	Ras-related protein Rab-1A × 1 （P62820） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.288

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 4IRU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4I1M Crystal structure of the Legionella pneumophila GAP domain of LepB Deposited 2012-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 317–618（302 aa） Fragment：GAP domain (UNP residues 317-618)	Mutation：K457A, E458A, K460A	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bicine, pH 7.5, 0.75 M lithium chloride, 6% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.238
4I1M Crystal structure of the Legionella pneumophila GAP domain of LepB Deposited 2012-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 317–618（302 aa） Fragment：GAP domain (UNP residues 317-618)	Mutation：K457A, E458A, K460A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bicine, pH 7.5, 0.75 M lithium chloride, 6% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.238
4I1M Crystal structure of the Legionella pneumophila GAP domain of LepB Deposited 2012-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 317–618（302 aa） Fragment：GAP domain (UNP residues 317-618)	Mutation：K457A, E458A, K460A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bicine, pH 7.5, 0.75 M lithium chloride, 6% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.238
4I1O Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3 Deposited 2012-11-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 317–618（302 aa） Fragment：GAP domain (UNP residues 317-618)	Mutation：K457A, E458A, K460A	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249
4I1O Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3 Deposited 2012-11-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 317–618（302 aa） Fragment：GAP domain (UNP residues 317-618)	Mutation：K457A, E458A, K460A	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249
4I1O Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3 Deposited 2012-11-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 317–618（302 aa） Fragment：GAP domain (UNP residues 317-618)	Mutation：K457A, E458A, K460A	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249
4I1O Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3 Deposited 2012-11-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 317–618（302 aa） Fragment：GAP domain (UNP residues 317-618)	Mutation：K457A, E458A, K460A	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249

2 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5ZSM7_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–299； UniProt 326–623 Author chain C； PDBConstruct 2–299； UniProt 326–623 Author chain E； PDBConstruct 2–299； UniProt 326–623

Ras-related protein Rab-1A

Homo sapiens

UniProt P62820

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 4–177	Non-standard monomer：Yes (specific site not provided by mmCIF)	LepB × 1 （Q5ZSM7） ACT ACETATE ION × 4 GOL GLYCEROL × 7 K POTASSIUM ION × 5 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.288
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 4–177	Non-standard monomer：Yes (specific site not provided by mmCIF)	LepB × 1 （Q5ZSM7） ACT ACETATE ION × 8 GOL GLYCEROL × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.288
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 4–177	Non-standard monomer：Yes (specific site not provided by mmCIF)	LepB × 1 （Q5ZSM7） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.288

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 4IRU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FOL Crystal structure of human RAB1A in complex with GDP Deposited 2006-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–176（172 aa）	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 UNX UNKNOWN LIGAND × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% PEG3350, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K	Resolution 2.63 Å R-free 0.252
2WWX Crystal structure of the SidM/DrrA(GEF/GDF domain)-Rab1(GTPase domain) complex Deposited 2009-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 4–178（175 aa） Fragment：GTPASE DOMAIN, RESIDUES 4-178	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å R-free 0.231
3L0I Complex structure of SidM/DrrA with the wild type Rab1 Deposited 2009-12-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–177（177 aa） Fragment：small GTPase domain, residues 1-177	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；1.1M ammonium sulfate, 0.1M sodium citrate, 0.4M Li2SO4, 0.1M di-ammonium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.85 Å R-free 0.266
3L0I Complex structure of SidM/DrrA with the wild type Rab1 Deposited 2009-12-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–177（177 aa） Fragment：small GTPase domain, residues 1-177	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；1.1M ammonium sulfate, 0.1M sodium citrate, 0.4M Li2SO4, 0.1M di-ammonium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.85 Å R-free 0.266
3SFV Crystal structure of the GDP-bound Rab1a S25N mutant in complex with the coiled-coil domain of LidA from Legionella pneumophila Deposited 2011-06-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–176（176 aa） Fragment：residues 1-176	Mutation：S25N	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；293 K；28% Jeffamin ED-2001, 0.1M sodium citrate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.73 Å R-free 0.228
3TKL Crystal structure of the GTP-bound Rab1a in complex with the coiled-coil domain of LidA from Legionella pneumophila Deposited 2011-08-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa） Fragment：UNP residues 1-191	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 25% PEG3350, 0.7% butanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.18 Å R-free 0.252
4FMB VirA-Rab1 complex structure Deposited 2012-06-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 6–176（171 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.247
4FMB VirA-Rab1 complex structure Deposited 2012-06-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 6–176（171 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.247
4FMB VirA-Rab1 complex structure Deposited 2012-06-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 6–176（171 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.247
4FMB VirA-Rab1 complex structure Deposited 2012-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 6–176（171 aa） Chain D 6–176（171 aa） Chain F 6–176（171 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.247
4FMC EspG-Rab1 complex Deposited 2012-06-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 6–176（171 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；20% PEG3350 and 0.1 M potassium sodium tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.277
4FMC EspG-Rab1 complex Deposited 2012-06-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 6–176（171 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；20% PEG3350 and 0.1 M potassium sodium tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.277
4FMC EspG-Rab1 complex Deposited 2012-06-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 14–115（102 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；20% PEG3350 and 0.1 M potassium sodium tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.277
4FMD EspG-Rab1 complex structure at 3.05 A Deposited 2012-06-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 6–176（171 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；20% PEG3350, 0.1 M trisodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.05 Å R-free 0.266
4FMD EspG-Rab1 complex structure at 3.05 A Deposited 2012-06-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 6–176（171 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；20% PEG3350, 0.1 M trisodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.05 Å R-free 0.266
4FMD EspG-Rab1 complex structure at 3.05 A Deposited 2012-06-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 13–176（164 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；20% PEG3350, 0.1 M trisodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.05 Å R-free 0.266
4FME EspG-Rab1-Arf6 complex Deposited 2012-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 6–176（171 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；298 K；8% PEG8000, 0.1 M NaKPO4 (pH 6.2), and 0.2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.10 Å R-free 0.249
4FME EspG-Rab1-Arf6 complex Deposited 2012-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 6–176（171 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；298 K；8% PEG8000, 0.1 M NaKPO4 (pH 6.2), and 0.2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.10 Å R-free 0.249
4JVS Crystal structure of LepB GAP domain from Legionella drancourtii in complex with Rab1-GDP and AlF3 Deposited 2013-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–177（177 aa） Fragment：UNP residues 1-177	Not recorded	ACY ACETIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；298 K；0.2M ammonium acetate, 0.1M Tris, 25%(w/v) polyethylene glycol 3350, pH 8.5, EVAPORATION, temperature 298.0K	Resolution 2.78 Å R-free 0.265
7EQ2 Crystal structure of GDP-bound Rab1a-T75D Deposited 2021-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–176（176 aa）	Mutation：T75D	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NCO COBALT HEXAMMINE(III) × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；291.15 K；40mM Lithium chloride, 20mM Magnesium chloride hexahydrate, 80mM NaCl, 2mM Hexammine cobalt(III) chloride, 40mM Sodium cacodylate trihydrate pH 5.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol	Resolution 1.55 Å R-free 0.185
7EQ2 Crystal structure of GDP-bound Rab1a-T75D Deposited 2021-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–176（176 aa）	Mutation：T75D	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NCO COBALT HEXAMMINE(III) × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CAC CACODYLATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；291.15 K；40mM Lithium chloride, 20mM Magnesium chloride hexahydrate, 80mM NaCl, 2mM Hexammine cobalt(III) chloride, 40mM Sodium cacodylate trihydrate pH 5.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol	Resolution 1.55 Å R-free 0.185
9MHF Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L) Deposited 2024-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–205（205 aa）	Mutation：Q70L	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9MHG Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation Deposited 2024-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–205（205 aa）	Mutation：Q70L	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；OG supplemented at time of grid preparation 0.05% cryo-EM vitrification conditions Cryogen ETHANE；100% humidity, 3 s wait time, blot force -15	Resolution 3.20 Å
9MHH PI3KC3-C1 in complex with RAB1A. VPS34 kinase domain active conformation Deposited 2024-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–205（205 aa）	Mutation：Q70L	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；OG supplemented at time of grid preparation 0.05% cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å

14 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAB1A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 11–184； UniProt 4–177 Author chain D； PDBConstruct 11–184； UniProt 4–177 Author chain F； PDBConstruct 11–184； UniProt 4–177

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4iru
Deposition date deposition_date	2013-01-15
Structure title title	Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3
Keywords keywords	;Arginine finger, Glutamate finger, P-loop motif, Nucleotide binding, Intrinsic GTPase activity, GTP hydrolysis, GTP hydrolysis activator, GTPase activating protein (GAP), Protein transport, HYDROLASE-HYDROLASE complex ;; HYDROLASE/HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	41.74 Å
Radius of gyration Rg (electron density) rg_electron	41.31 Å
Forward intensity I(0) i0	376904000.00
Molecular weight molecular_weight	162590.0 kDa
Excluded volume excluded_volume	204510 Å³
Envelope volume envelope_volume	274530 Å³
Hydration-shell volume shell_volume	55545 Å³
Envelope diameter envelope_diameter	146.7 Å
Shell Rg shell_rg	46.59 Å
Envelope Rg envelope_rg	40.67 Å
Shape Rg shape_rg	41.26 Å
Total Rg total_rg	41.75 Å
Total atoms total_atoms	11376
Residues n_residues	1379
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	135.3 Å
Rg (real space) rg_real	41.65 Å
Rg uncertainty (real space) rg_real_error	1.19 Å
I(0) (real space) i0_real	3.7690e+08
I(0) uncertainty (real space) i0_real_error	6.3790e+06
Rg (reciprocal space) rg_reciprocal	41.74 Å
I(0) (reciprocal space) i0_reciprocal	376900000.0000
Solution quality estimate total_estimate	0.6843
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	53.4 Å
Skewness Skewness skewness	0.133
Kurtosis Kurtosis kurtosis	-0.679
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31450000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 0.046; Positv: 1.000; Valcen: 0.999; Smooth: 0.947

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	LepB
Molecular weight formula_weight	33916.3 kDa
EC 编号 ec_number	3.6.5.2
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	11410

SLKPLTLLMTSSTSFSETINQWADILKTTDMEKFSFDSNPINLLELVKQFNLYVDELAITCEANNVWAKERIDSTPNLFALYDNSGGEAIHGHAFVPYYKESIVLRRLFTVDPNTFNLSRFAAFEGPCQLYCKEHKDSAWVKIQTLLTLGNGIINTLKIIKQAQAFGIDEAVTENLKALKEQFIAFQLAEADIKESLKAPSFAEPLPNKESEFFYPIDEKALAKMNGYQLATICLEELNSPKPSPLIERILSNKKFWKRINSAFESGVFKGRTDDPAGKIAKIREWHQLLQISGKKTAG

来源 Source

来源生物 organism	Legionella pneumophila
NCBI Class编号 ncbi_taxonomy_id	272624
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ras-related protein Rab-1A
Molecular weight formula_weight	21175.2 kDa
EC 编号 ec_number	3.6.5.2
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

MGHHHHHHGSMNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRMG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	ALUMINUM FLUORIDE
Molecular weight formula_weight	84.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

▼

7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	4iruA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1700 —

Domain ID domain_id	4iruA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	830 —

Domain ID domain_id	4iruB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4iruC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1700 —

Domain ID domain_id	4iruC02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	830 —

Domain ID domain_id	4iruD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4iruE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1700 —

Domain ID domain_id	4iruE02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	830 —

Domain ID domain_id	4iruF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

▶

8. Citations (1)

▶

Unit-cell length a length_a	139.404 Å
Unit-cell length b length_b	139.404 Å
Unit-cell length c length_c	384.519 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	43.010 Å
R factor r_factor	0.2325
R_work r_work	0.2295
R_free r_free	0.2881

fit	/app/data/saxs_computation/ir/4iru/4iru.fit
pddf	/app/data/pr_computation/ir/4iru/4iru.pr.out
profile	/app/data/saxs_computation/ir/4iru/4iru.dat

Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3

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

LepB

State in the Current Structure

Other States of the Same Protein in the Database

Ras-related protein Rab-1A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)