SAXSdb — 2al7

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

ADP-ribosylation factor-like 10C

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 18–184	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG 3350 25%, Ammonium Acetate 100mM, 100mM HEPES (7.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.85 Å R-free 0.251

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 2AL7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8JC5 Crystal structure of PLEKHM1 RUN domain in complex with GTP-bound Arl8b(Q75L) Deposited 2023-05-10	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 18–186（169 aa）	Mutation：Q75L	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Lithium chloride, 0.1 M TRIS pH=7.6, 18% (w/v) PEG 8000	Resolution 2.01 Å R-free 0.201
8JC5 Crystal structure of PLEKHM1 RUN domain in complex with GTP-bound Arl8b(Q75L) Deposited 2023-05-10	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 B 18–186（169 aa）	Mutation：Q75L	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Lithium chloride, 0.1 M TRIS pH=7.6, 18% (w/v) PEG 8000	Resolution 2.01 Å R-free 0.201
8JCA Cyrstal structure of SKIP RUN domain in complex with GTP-bound Arl8b(Q75L) Deposited 2023-05-10	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 18–186（169 aa）	Mutation：Q75L	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；800mM Potassiam phosphate dibasic 1.2 M Sodium phosphate monobasic 0.1M CAPS/Sodium hydroxide 0.2M Lithium sulfate pH10.5	Resolution 1.65 Å R-free 0.206

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

View Construct and Data Evidence

UniProt name	Q9NVJ2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–186； UniProt 18–184

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2al7
Deposition date deposition_date	2005-08-04
Structure title title	Structure Of Human ADP-Ribosylation Factor-Like 10C
Keywords keywords	TRANSPORT PROTEIN, GDP-BINDING, MEMBRANE TRAFFICKING, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC; TRANSPORT PROTEIN
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	16.07 Å
Radius of gyration Rg (electron density) rg_electron	14.62 Å
Forward intensity I(0) i0	6682360.00
Molecular weight molecular_weight	18249.0 kDa
Excluded volume excluded_volume	22717 Å³
Envelope volume envelope_volume	25457 Å³
Hydration-shell volume shell_volume	14380 Å³
Envelope diameter envelope_diameter	51.2 Å
Shell Rg shell_rg	20.91 Å
Envelope Rg envelope_rg	15.02 Å
Shape Rg shape_rg	14.62 Å
Total Rg total_rg	15.81 Å
Total atoms total_atoms	1274
Residues n_residues	155
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	51.1 Å
Rg (real space) rg_real	15.94 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	6.6820e+06
I(0) uncertainty (real space) i0_real_error	7.6320e+04
Rg (reciprocal space) rg_reciprocal	15.95 Å
I(0) (reciprocal space) i0_reciprocal	6682000.0000
Solution quality estimate total_estimate	0.8060
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.067
Kurtosis Kurtosis kurtosis	-0.389
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1427000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ADP-ribosylation factor-like 10C
Molecular weight formula_weight	21204.4 kDa
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	1416

MGSSHHHHHHSSGLVPRGSKEEMELTLVGLQYSGKTTFVNVIASGQFSEDMIPTVGFNMRKVTKGNVTIKIWDIGGQPRFRSMWERYCRGVNAIVYMIDAADREKIEASRNELHNLLDKPQLQGIPVLVLGNKRDLPNALDEKQLIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHSKSR

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2al7a1
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

Domain ID domain_id	d2al7a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2al7A00
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	41.732 Å
Unit-cell length b length_b	62.393 Å
Unit-cell length c length_c	63.796 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	1.850 Å
Low-resolution limit resolution_low	44.590 Å
R factor r_factor	0.2032
R_work r_work	0.2007
R_free r_free	0.2506

fit	/app/data/saxs_computation/al/2al7/2al7.fit
pddf	/app/data/pr_computation/al/2al7/2al7.pr.out
profile	/app/data/saxs_computation/al/2al7/2al7.dat

Structure Of Human ADP-Ribosylation Factor-Like 10C

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

ADP-ribosylation factor-like 10C

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