SAXSdb — 5khq

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

Ras-interacting protein 1

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 134–285 Chain B； UniProt 134–285	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；1.5M Ammonium Sulfate and MES pH 6.0	Resolution 2.80 Å R-free 0.262

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 5KHQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5KHO Rasip1 RA domain in complex with Rap1B Deposited 2016-06-15	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 134–285（152 aa） Chain B 134–285（152 aa）	Not recorded	GOL GLYCEROL × 1 MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；16% PEG 8K, 200mM Calcium Acetate, and 100mM MES pH 6.5	Resolution 2.78 Å R-free 0.286

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

View Construct and Data Evidence

UniProt name	RAIN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–156； UniProt 134–285 Author chain B； PDBConstruct 5–156； UniProt 134–285

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	5khq
Deposition date deposition_date	2016-06-15
Structure title title	Rasip1 RA domain
Keywords keywords	Rasip1, Ras-Association domain, Rap effector, SIGNALING PROTEIN; SIGNALING 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	17.80 Å
Radius of gyration Rg (electron density) rg_electron	16.92 Å
Forward intensity I(0) i0	9287150.00
Molecular weight molecular_weight	22149.0 kDa
Excluded volume excluded_volume	27693 Å³
Envelope volume envelope_volume	32827 Å³
Hydration-shell volume shell_volume	16365 Å³
Envelope diameter envelope_diameter	57.9 Å
Shell Rg shell_rg	22.74 Å
Envelope Rg envelope_rg	17.13 Å
Shape Rg shape_rg	16.90 Å
Total Rg total_rg	17.96 Å
Total atoms total_atoms	1564
Residues n_residues	200
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	59.1 Å
Rg (real space) rg_real	17.72 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	9.2870e+06
I(0) uncertainty (real space) i0_real_error	1.1000e+05
Rg (reciprocal space) rg_reciprocal	17.73 Å
I(0) (reciprocal space) i0_reciprocal	9287000.0000
Solution quality estimate total_estimate	0.8748
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.275
Kurtosis Kurtosis kurtosis	-0.231
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3439000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ras-interacting protein 1
Molecular weight formula_weight	16345.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1573

GAMGEPPLATRATAPPGVLKIFGAGLASGANYKSVLATARSTARELVAEALERYGLAGSPGGGPGESSCVDAFALCDALGRPAAAGVGSGEWRAEHLRVLGDSERPLLVQELWRARPGWARRFELRGREEARRLEQEAFGAADSEGTGAPSWRPQK

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 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5khqA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	5khqB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	89.200 Å
Unit-cell length b length_b	89.200 Å
Unit-cell length c length_c	177.950 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	47.050 Å
R factor r_factor	0.2358
R_work r_work	0.2344
R_free r_free	0.2618

fit	/app/data/saxs_computation/kh/5khq/5khq.fit
pddf	/app/data/pr_computation/kh/5khq/5khq.pr.out
profile	/app/data/saxs_computation/kh/5khq/5khq.dat

Rasip1 RA domain

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

Ras-interacting protein 1

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