SAXSdb — 5xpy

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

Fermitin family homolog 2

Mus musculus

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 15–680	Fragment：UNP residues 15-680 Mutation：168-217 deletion, 367-512 deletion	ACT ACETATE ION × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.1 M Tris pH 8.5, 4.0 M Ammonium acetate	Resolution 2.10 Å R-free 0.196

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 5XPY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5XPZ Structural basis of kindlin-mediated integrin recognition and activation Deposited 2017-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–680（680 aa） Chain B 1–680（680 aa）	Mutation：168-217 deletion, 337-512 deletion Mutation：168-217 deletion, 337-512 deletion	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v pentaerythritol propoxylate	Resolution 2.60 Å R-free 0.283
5XQ0 Structural basis of kindlin-mediated integrin recognition and activation Deposited 2017-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–680（680 aa） Fragment：UNP residues 784-798 Chain B 1–680（680 aa） Fragment：UNP residues 784-798	Mutation：168-217 deletion, 337-512 deletion Mutation：168-217 deletion, 337-512 deletion	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v pentaerythritol propoxylate	Resolution 2.75 Å R-free 0.284
5XQ1 Structural basis of kindlin-mediated integrin recognition and activation Deposited 2017-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–680（680 aa） Fragment：UNP residues 773-787 Chain B 1–680（680 aa） Fragment：UNP residues 773-787	Mutation：168-217 deletion, 337-512 deletion Mutation：168-217 deletion, 337-512 deletion	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v pentaerythritol propoxylate	Resolution 2.95 Å R-free 0.260
8TEC Crystal structure of Kindlin2 in complex with acylated beta1 integrin peptide Deposited 2023-07-06	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 A 1–336（336 aa） Fragment：UNP residues 1-336,513-680 Chain A 513–680（168 aa） Fragment：UNP residues 1-336,513-680 Chain B 1–336（336 aa） Fragment：UNP residues 1-336,513-680 Chain B 513–680（168 aa） Fragment：UNP residues 1-336,513-680	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1 M Tris, pH 8.5, 10% isopropanal	Resolution 2.04 Å R-free 0.230
8TEE Crystal structure of Kindlin2 in complex with K794Q mutated beta1 integrin Deposited 2023-07-06	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 1–336（336 aa） Fragment：UNP residues 1-336,513-680 Chain A 513–680（168 aa） Fragment：UNP residues 1-336,513-680 Chain B 1–336（336 aa） Fragment：UNP residues 1-336,513-680 Chain B 513–680（168 aa） Fragment：UNP residues 1-336,513-680	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Tris, pH 8.5, 10% isopropanal	Resolution 2.49 Å R-free 0.275

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FERM2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–474； UniProt 15–680

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	5xpy
Deposition date deposition_date	2017-06-05
Structure title title	Structural basis of kindlin-mediated integrin recognition and activation
Keywords keywords	Integrin Binding, Multi-domain containing protein, 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	27.19 Å
Radius of gyration Rg (electron density) rg_electron	26.37 Å
Forward intensity I(0) i0	44544900.00
Molecular weight molecular_weight	52794.0 kDa
Excluded volume excluded_volume	66597 Å³
Envelope volume envelope_volume	83900 Å³
Hydration-shell volume shell_volume	27859 Å³
Envelope diameter envelope_diameter	109.0 Å
Shell Rg shell_rg	32.17 Å
Envelope Rg envelope_rg	26.94 Å
Shape Rg shape_rg	26.33 Å
Total Rg total_rg	27.16 Å
Total atoms total_atoms	3713
Residues n_residues	454
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	102.0 Å
Rg (real space) rg_real	27.30 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	4.4540e+07
I(0) uncertainty (real space) i0_real_error	7.2220e+05
Rg (reciprocal space) rg_reciprocal	27.27 Å
I(0) (reciprocal space) i0_reciprocal	44540000.0000
Solution quality estimate total_estimate	0.8258
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.477
Kurtosis Kurtosis kurtosis	-0.093
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14260000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.650; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.822; Smooth: 0.957

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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	Fermitin family homolog 2
Molecular weight formula_weight	55083.3 kDa
Mutation mutation	168-217 deletion, 367-512 deletion
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	3912

HMGSDGTWELSVHVTDLNRDVTLRVTGEVHIGGVMLKLVEKLDVKKDWSDHALWWEKKRTWLLKTHWTLDKCGIQADAKLQFTPQHKLLRLQLPNMKYVKVKVNFSDRVFKAVSDICKTFNIRHPEELSLLKKPRDPTKKKKKKLDDQSEDEALELEPGILAVSQPVTSPEILAKMFKPQALLDKAKTNQGWLDSSRSLMEQDVKENEALLLRFKYYSFFDLNPKYDAIRINQLYEQAKWALLLEEIECTEEEMMMFAALQYHINKLSIMTSENHLNNSDKEVDEVDAALSDLEITLEGGKTSTILTTDVNPECLVSPRYLKKYKSKQITARILEAHQNVAQMSLIEAKMRFIQAWQSLPEFGITHFIARFQGGKREELIGIAYNRLIRMDASTGDAIKTWRFSNMKQWNVNWEIKMVTVEFADEVRLSFICTEVDCKVVHEFIGGYIFLSTRAKDQNESLDEEMFYKLTSGWV

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	156

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5xpyA01
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	5xpyA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	145.069 Å
Unit-cell length b length_b	145.069 Å
Unit-cell length c length_c	59.352 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.099 Å
Low-resolution limit resolution_low	31.408 Å
R factor r_factor	0.1655
R_work r_work	0.1640
R_free r_free	0.1959

fit	/app/data/saxs_computation/xp/5xpy/5xpy.fit
pddf	/app/data/pr_computation/xp/5xpy/5xpy.pr.out
profile	/app/data/saxs_computation/xp/5xpy/5xpy.dat

Structural basis of kindlin-mediated integrin recognition and activation

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

Fermitin family homolog 2

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