SAXSdb — 5lpn

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

Ras-related protein Rab-10

Homo sapiens

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–175 Chain C； UniProt 1–175	Not recorded	Protein-methionine sulfoxide oxidase MICAL1 × 1 （Q8TDZ2） MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；6%-10% PEG8000 0.1M Imidazole	Resolution 2.80 Å R-free 0.287

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 5LPN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5SZJ Structure of human Rab10 in complex with the bMERB domain of Mical-cL Deposited 2016-08-14	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 1–200（200 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；18%-22% PEG 3350 0.2-0.3 M Sodium Acetate	Resolution 2.66 Å R-free 0.266
9G0C Structure of human Mical1 bMERB_V978A_V985A domain:Rab10 complex. Deposited 2024-07-08	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 B 1–175（175 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.17 M Sodium acetate, 0.085 M Tris-HCl pH 8.5, 25.5% (w/v) PEG 4000 and 15% (v/v) glycerol	Resolution 1.80 Å R-free 0.231
9G0D Structure of human Mical1 bMERB_V978A domain:Rab10 complex. Deposited 2024-07-08	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 C 1–175（175 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Imidazole pH 8.0, 5% (w/v) PEG 3000 and 30% (v/v) PEG 200	Resolution 2.05 Å R-free 0.249

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

View Construct and Data Evidence

UniProt name	RAB10_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–177； UniProt 1–175 Author chain C； PDBConstruct 3–177； UniProt 1–175

Protein-methionine sulfoxide oxidase MICAL1

Homo sapiens

UniProt Q8TDZ2

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 918–1067	Fragment：UNP residues 918-1067	Ras-related protein Rab-10 × 2 （P61026） MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；6%-10% PEG8000 0.1M Imidazole	Resolution 2.80 Å R-free 0.287

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 5LPN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WYL Solution structure of the CH domain of human NEDD9 interacting protein with calponin homology and LIM domains Deposited 2005-02-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 510–612（103 aa） Fragment：CH domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.22mM CH domain U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2CO8 Solution structures of the LIM domain of human NEDD9 interacting protein with calponin homology and LIM domains Deposited 2005-05-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 687–755（69 aa） Fragment：LIM domain	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1mM LIM domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.01mM ZnCl2; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2DK9 Solution structure of Calponin Homology domain of Human MICAL-1 Deposited 2006-04-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 506–614（109 aa） Fragment：Calponin Homology domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 50mM phosphate buffer, 50mM NaCl；Pressure 1 NMR sample composition 1.5mM MICAL_1 CH U-15N,13C; 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.5mM MICAL_1 CH U-15N; 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.5mM MICAL_1 CH U-15N,13C; 50mM phosphate buffer, 50mM NaCl; 100% D2O \| 100% D2O NMR sample composition 1.5mM MICAL_1 CH U-15N; 50mM phosphate buffer, 50mM NaCl; 17 mg/mL Pf1 filamentous phage; 90% H2O, 10% D2O \| 17 mg/mL Pf1 filamentous phage; 90% H2O, 10% D2O	Resolution not provided
5LE0 MICAL1 Cterminal domain Deposited 2016-06-29	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 B 918–1067（150 aa） Fragment：UNP residues 918-1067	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；EG	Resolution 3.30 Å R-free 0.306
6KU0 Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM Deposited 2019-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 799–822（24 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1% w/v Tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3350	Resolution 1.60 Å R-free 0.199
6KU0 Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM Deposited 2019-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 799–822（24 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1% w/v Tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3350	Resolution 1.60 Å R-free 0.199
8HLO Crystal structure of ASAP1-SH3 and MICAL1-PRM complex Deposited 2022-11-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 828–836（9 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；289.15 K；0.1M HEPES, pH 7.5, 1.4M Sodium citrate tribasic dihydrate	Resolution 1.17 Å R-free 0.142
8Y6K Cryo-EM structure of full-length MICAL1 in the autoinhibited state Deposited 2024-02-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1067（1067 aa）	Not recorded	ZN ZINC ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris, pH 7.5, 100 mM NaCl, 2 mM MgCl2, 2 mM DTT. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å
9EWY CryoEM structure of human MICAL1 Deposited 2024-04-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1067（1067 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9G0C Structure of human Mical1 bMERB_V978A_V985A domain:Rab10 complex. Deposited 2024-07-08	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 918–1067（150 aa）	Mutation：V978A, V985A	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.17 M Sodium acetate, 0.085 M Tris-HCl pH 8.5, 25.5% (w/v) PEG 4000 and 15% (v/v) glycerol	Resolution 1.80 Å R-free 0.231
9G0D Structure of human Mical1 bMERB_V978A domain:Rab10 complex. Deposited 2024-07-08	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 B 918–1067（150 aa）	Mutation：V978A	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Imidazole pH 8.0, 5% (w/v) PEG 3000 and 30% (v/v) PEG 200	Resolution 2.05 Å R-free 0.249

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MICA1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–153； UniProt 918–1067

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5lpn
Deposition date deposition_date	2016-08-14
Structure title title	Structure of human Rab10 in complex with the bMERB domain of Mical-1
Keywords keywords	Mical-1, DUF3585, Mical, Rab effector, Rab10, oxidoreductase, endocytosis; ENDOCYTOSIS
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	28.87 Å
Radius of gyration Rg (electron density) rg_electron	28.02 Å
Forward intensity I(0) i0	48309100.00
Molecular weight molecular_weight	53322.0 kDa
Excluded volume excluded_volume	66519 Å³
Envelope volume envelope_volume	84791 Å³
Hydration-shell volume shell_volume	26465 Å³
Envelope diameter envelope_diameter	98.4 Å
Shell Rg shell_rg	33.65 Å
Envelope Rg envelope_rg	27.83 Å
Shape Rg shape_rg	27.99 Å
Total Rg total_rg	28.69 Å
Total atoms total_atoms	3743
Residues n_residues	470
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	93.7 Å
Rg (real space) rg_real	29.00 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	4.8310e+07
I(0) uncertainty (real space) i0_real_error	7.8860e+05
Rg (reciprocal space) rg_reciprocal	28.95 Å
I(0) (reciprocal space) i0_reciprocal	48310000.0000
Solution quality estimate total_estimate	0.8687
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.603
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8239000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.833; Smooth: 0.939

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Ras-related protein Rab-10
Molecular weight formula_weight	20202.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3747

GHMAKKTYDLLFKLLLIGDSGVGKTCVLFRFSDDAFNTTFISTIGIDFKIKTVELQGKKIKLQIWDTAGQERFHTITTSYYRGAMGIMLVYDITNGKSFENISKWLRNIDEHANEDVERMLLGNKCDMDDKRVVPKGKGEQIAREHGIRFFETSAKANINIEKAFLTLAEDILRKTP

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 2 Entity 2 polymer

Description description	Protein-methionine sulfoxide oxidase MICAL1
Molecular weight formula_weight	17852.3 kDa
EC 编号 ec_number	1.14.13.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GHMKEEEMKRFCKAQTIQRRLNEIEAALRELEAEGVKLELALRRQSSSPEQQKKLWVGQLLQLVDKKNSLVAEEAELMITVQELNLEEKQWQLDQELRGYMNREENLKTAADRQAEDQVLRKLVDLVNQRDALIRFQEERRLSELALGTGAQG

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5lpna_
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.37.1.0 — automated matches

Domain ID domain_id	d5lpnc_
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.37.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5lpnA00
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	5lpnC00
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	58.390 Å
Unit-cell length b length_b	59.000 Å
Unit-cell length c length_c	198.180 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	8

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	44.004 Å
R factor r_factor	0.2462
R_work r_work	0.2440
R_free r_free	0.2866

fit	/app/data/saxs_computation/lp/5lpn/5lpn.fit
pddf	/app/data/pr_computation/lp/5lpn/5lpn.pr.out
profile	/app/data/saxs_computation/lp/5lpn/5lpn.dat

Structure of human Rab10 in complex with the bMERB domain of Mical-1

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

Ras-related protein Rab-10

State in the Current Structure

Other States of the Same Protein in the Database

Protein-methionine sulfoxide oxidase MICAL1

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 (5)

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 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)