1n6k

Crystal Structure of Human Rab5a A30P mutant complex with GDP and aluminum fluoride

Method: X-RAY DIFFRACTION D_max: 52.6 Å Quality: GOOD

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

Ras-related protein Rab-5A

Homo sapiens

UniProt P20339

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 15–184	Fragment：GTPASE DOMAIN Mutation：A30P	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.200

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 1N6K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1N6H Crystal Structure of Human Rab5a Deposited 2002-11-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–184（170 aa） Fragment：GTPASE DOMAIN	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.51 Å R-free 0.190
1N6I Crystal Structure of Human Rab5a A30P mutant Complex with GDP Deposited 2002-11-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–184（170 aa） Fragment：GTPASE DOMAIN	Mutation：A30P	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.214
1N6L Crystal Structure of Human Rab5a A30P mutant complex with GTP Deposited 2002-11-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–184（170 aa） Fragment：GTPASE DOMAIN	Mutation：A30P	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.211
1N6N Crystal Structure of Human Rab5a A30R mutant complex with GppNHp Deposited 2002-11-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–184（170 aa） Fragment：GTPASE DOMAIN	Mutation：A30R	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.207
1N6O Crystal Structure of Human Rab5a A30K mutant complex with GppNHp Deposited 2002-11-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–184（170 aa） Fragment：GTPASE DOMAIN	Mutation：A30K	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.207
1N6P Crystal Structure of Human Rab5a A30E mutant complex with GppNHp Deposited 2002-11-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–184（170 aa） Fragment：GTPASE DOMAIN	Mutation：A30E	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.54 Å R-free 0.204
1N6R Crystal Structure of Human Rab5a A30L mutant complex with GppNHp Deposited 2002-11-11	Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–184（170 aa） Fragment：GTPASE DOMAIN	Mutation：A30L	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 6000, sodium chloride, MES , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.55 Å R-free 0.200
1R2Q Crystal Structure of Human Rab5a GTPase Domain at 1.05 A resolution Deposited 2003-09-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–184（170 aa） Fragment：GTPase domain	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 6000, SODIUM CHLORIDE, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.05 Å R-free 0.169
1TU3 Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain Deposited 2004-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 15–184（170 aa） Chain B 15–184（170 aa）	Not recorded	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG3350, ammonium bromide, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.31 Å R-free 0.277
1TU3 Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain Deposited 2004-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 15–184（170 aa） Chain D 15–184（170 aa）	Not recorded	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG3350, ammonium bromide, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.31 Å R-free 0.277
1TU3 Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain Deposited 2004-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 15–184（170 aa）	Not recorded	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG3350, ammonium bromide, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.31 Å R-free 0.277
1TU4 Crystal Structure of Rab5-GDP Complex Deposited 2004-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–184（170 aa） Fragment：GTP binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
1TU4 Crystal Structure of Rab5-GDP Complex Deposited 2004-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 15–184（170 aa） Fragment：GTP binding domain Chain B 15–184（170 aa） Fragment：GTP binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
1TU4 Crystal Structure of Rab5-GDP Complex Deposited 2004-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 15–184（170 aa） Fragment：GTP binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
1TU4 Crystal Structure of Rab5-GDP Complex Deposited 2004-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 15–184（170 aa） Fragment：GTP binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
1TU4 Crystal Structure of Rab5-GDP Complex Deposited 2004-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 15–184（170 aa） Fragment：GTP binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
1TU4 Crystal Structure of Rab5-GDP Complex Deposited 2004-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 15–184（170 aa） Fragment：GTP binding domain Chain B 15–184（170 aa） Fragment：GTP binding domain Chain C 15–184（170 aa） Fragment：GTP binding domain Chain D 15–184（170 aa） Fragment：GTP binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 12 GDP GUANOSINE-5'-DIPHOSPHATE × 8 SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
1TU4 Crystal Structure of Rab5-GDP Complex Deposited 2004-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 15–184（170 aa） Fragment：GTP binding domain Chain B 15–184（170 aa） Fragment：GTP binding domain Chain C 15–184（170 aa） Fragment：GTP binding domain Chain D 15–184（170 aa） Fragment：GTP binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 4 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
1TU4 Crystal Structure of Rab5-GDP Complex Deposited 2004-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 15–184（170 aa） Fragment：GTP binding domain Chain B 15–184（170 aa） Fragment：GTP binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
1TU4 Crystal Structure of Rab5-GDP Complex Deposited 2004-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 15–184（170 aa） Fragment：GTP binding domain Chain D 15–184（170 aa） Fragment：GTP binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 4 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
1TU4 Crystal Structure of Rab5-GDP Complex Deposited 2004-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 15–184（170 aa） Fragment：GTP binding domain Chain D 15–184（170 aa） Fragment：GTP binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CO COBALT (II) ION × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
3MJH Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1 Deposited 2010-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 16–183（168 aa） Fragment：residues 16-183	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；18% PEG 4000, 50mM sodium acetate, 0.2M sodium-potassium phosphate, 10% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 2.03 Å R-free 0.260
3MJH Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1 Deposited 2010-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 16–183（168 aa） Fragment：residues 16-183	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；18% PEG 4000, 50mM sodium acetate, 0.2M sodium-potassium phosphate, 10% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 2.03 Å R-free 0.260
4Q9U Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex Deposited 2014-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 15–184（170 aa） Fragment：UNP residues 15-184 Chain F 15–184（170 aa） Fragment：UNP residues 15-184	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 5；289 K；1.0M NaH2PO4/K2HPO4, pH 5.0, hanging drop, temperature 289K	Resolution 4.62 Å R-free 0.343
7BL1 human complex II-BATS bound to membrane-attached Rab5a-GTP Deposited 2021-01-17	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 × 6 PDB declaration: hexameric	Chain DDD 16–183（168 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot force 20, blot time 6 s	Resolution 9.80 Å
9RX5 VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L) Deposited 2025-07-10	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 × 6 PDB declaration: hexameric	Chain E 1–212（212 aa） Chain F 1–212（212 aa）	Mutation：C19A, C63S, Q79L Mutation：C19A, C63S, Q79L	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.15 Å
9RX6 VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit Deposited 2025-07-10	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 F 1–212（212 aa）	Mutation：C19S, C63S, Q79L	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.52 Å
9RX9 VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit Deposited 2025-07-10	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 1–212（212 aa）	Mutation：C19S, C63S, Q79L	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.99 Å
9RXA VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS15 subunit Deposited 2025-07-10	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 F 1–212（212 aa）	Mutation：C19S, C63S, Q79L	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 4.00 Å
9RXB VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) bound to RAB5A (Q79L) on the VPS34 and VPS15 subunits Deposited 2025-07-10	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 × 6 PDB declaration: hexameric	Chain E 1–212（212 aa） Chain F 1–212（212 aa）	Mutation：C19S, C63S, Q79L Mutation：C19S, C63S, Q79L	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 4.03 Å
9S47 Human complex II-BATS bound to membrane-attached Rab5a-GTP Deposited 2025-07-25	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 1–212（212 aa）	Mutation：C19S, C63S, Q79L	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 9.88 Å

19 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAB5A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–170； UniProt 15–184

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1n6k
Deposition date deposition_date	2002-11-11
Structure title title	Crystal Structure of Human Rab5a A30P mutant complex with GDP and aluminum fluoride
Keywords keywords	Rab, GTPase, protein transport; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	16.47 Å
Radius of gyration Rg (electron density) rg_electron	15.14 Å
Forward intensity I(0) i0	7223500.00
Molecular weight molecular_weight	19265.0 kDa
Excluded volume excluded_volume	23958 Å³
Envelope volume envelope_volume	26453 Å³
Hydration-shell volume shell_volume	14612 Å³
Envelope diameter envelope_diameter	53.7 Å
Shell Rg shell_rg	21.27 Å
Envelope Rg envelope_rg	15.53 Å
Shape Rg shape_rg	15.10 Å
Total Rg total_rg	16.33 Å
Total atoms total_atoms	1349
Residues n_residues	167
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

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

Maximum dimension Dmax dmax	52.6 Å
Rg (real space) rg_real	16.36 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	7.2240e+06
I(0) uncertainty (real space) i0_real_error	7.8490e+04
Rg (reciprocal space) rg_reciprocal	16.37 Å
I(0) (reciprocal space) i0_reciprocal	7224000.0000
Solution quality estimate total_estimate	0.8111
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.126
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1273000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ras-related protein Rab-5A
Molecular weight formula_weight	19013.6 kDa
Mutation mutation	A30P
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1627

GNKICQFKLVLLGESPVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKN

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ALUMINUM FLUORIDE
Molecular weight formula_weight	84.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1n6ka_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (1 domains)

Domain ID domain_id	1n6kA00
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

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8. Citations (1)

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Unit-cell length a length_a	35.840 Å
Unit-cell length b length_b	64.040 Å
Unit-cell length c length_c	65.880 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1800
R_work r_work	0.1770
R_free r_free	0.2000

fit	/app/data/saxs_computation/n6/1n6k/1n6k.fit
pddf	/app/data/pr_computation/n6/1n6k/1n6k.pr.out
profile	/app/data/saxs_computation/n6/1n6k/1n6k.dat