SAXSdb — 6iuh

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

ARF GTPase-activating protein GIT1

Rattus norvegicus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 645–770	Not recorded	Liprin-alpha-2 × 1 （O75334） IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.2M Potassium iodide, 0.1M MES pH 6.5, 25% w/v PEG 4000	Resolution 1.80 Å R-free 0.267
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 645–770	Not recorded	Liprin-alpha-2 × 1 （O75334） IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.2M Potassium iodide, 0.1M MES pH 6.5, 25% w/v PEG 4000	Resolution 1.80 Å R-free 0.267

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 6IUH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JX0 The paxillin-binding domain (PBD) of G Protein Coupled Receptor (GPCR)-kinase (GRK) interacting protein 1 (GIT1) Deposited 2007-11-01	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 640–770（131 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 20；Pressure AMBIENT NMR sample composition 1.2 mM [U-99% 13C; U-99% 15N] GT, 20 mM potassium phosphate, 5 mM DTT, 5 mM EDTA, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2W6A X-ray Structure of the Dimeric GIT1 Coiled-Coil Domain Deposited 2008-12-17	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 426–483（58 aa） Fragment：COILED-COIL, RESIDUES 426-483 Chain B 426–483（58 aa） Fragment：COILED-COIL, RESIDUES 426-483	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M TRIS-HCL PH 8.5, 31% PEG 4000, 0.8M NACL	Resolution 1.40 Å R-free 0.199
6IUI Crystal structure of GIT1 PBD domain in complex with Paxillin LD4 motif Deposited 2018-11-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 645–770（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.1M HEPES pH 7.5, 30% w/v PEG 1000	Resolution 2.60 Å R-free 0.226
6IUI Crystal structure of GIT1 PBD domain in complex with Paxillin LD4 motif Deposited 2018-11-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 645–770（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.1M HEPES pH 7.5, 30% w/v PEG 1000	Resolution 2.60 Å R-free 0.226

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GIT1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–132； UniProt 645–770 Author chain B； PDBConstruct 7–132； UniProt 645–770

Liprin-alpha-2

Homo sapiens

UniProt O75334

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 642–671	Not recorded	ARF GTPase-activating protein GIT1 × 1 （Q9Z272） IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.2M Potassium iodide, 0.1M MES pH 6.5, 25% w/v PEG 4000	Resolution 1.80 Å R-free 0.267
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 642–671	Not recorded	ARF GTPase-activating protein GIT1 × 1 （Q9Z272） IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.2M Potassium iodide, 0.1M MES pH 6.5, 25% w/v PEG 4000	Resolution 1.80 Å R-free 0.267

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 6IUH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TAC Crystal Structure of the Liprin-alpha/CASK complex Deposited 2011-08-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 866–1193（328 aa） Fragment：UNP residues 866-1193	Not recorded	SO4 SULFATE ION × 7 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.4M ammonium sulfate, 0.2M NaCl, MES buffer, pH 6.5, vapor diffusion, hanging drop, temperature 289K	Resolution 2.20 Å R-free 0.236
3TAD Crystal Structure of the Liprin-alpha/Liprin-beta complex Deposited 2011-08-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 866–1193（328 aa） Fragment：UNP residues 866-975, 1113-1193	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K	Resolution 2.90 Å R-free 0.258
3TAD Crystal Structure of the Liprin-alpha/Liprin-beta complex Deposited 2011-08-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 866–1193（328 aa） Fragment：UNP residues 866-975, 1113-1193	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K	Resolution 2.90 Å R-free 0.258
7D2E Tetrameric coiled-coil structure of liprin-alpha2_H3 Deposited 2020-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 164–235（72 aa） Fragment：UNP residues 164-235 Chain B 164–235（72 aa） Fragment：UNP residues 164-235 Chain C 164–235（72 aa） Fragment：UNP residues 164-235 Chain D 164–235（72 aa） Fragment：UNP residues 164-235	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, 10% w/v Polyethylene glycol 6,000	Resolution 1.70 Å R-free 0.269
7D2G Coiled-coil structure of liprin-alpha2_H2delC Deposited 2020-09-16	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 102–150（49 aa） Fragment：UNP residues 102-150 Chain B 102–150（49 aa） Fragment：UNP residues 102-150	Mutation：L106M, C143A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L106M, C143A 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, SITTING DROP；289 K；0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350	Resolution 1.70 Å R-free 0.263
7D2G Coiled-coil structure of liprin-alpha2_H2delC Deposited 2020-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 102–150（49 aa） Fragment：UNP residues 102-150 Chain D 102–150（49 aa） Fragment：UNP residues 102-150	Mutation：L106M, C143A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L106M, C143A Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350	Resolution 1.70 Å R-free 0.263
7D2H Tetrameric coiled-coil structure of liprin-alpha2_H2 Deposited 2020-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 102–163（62 aa） Fragment：UNP residues 102-163 Chain B 102–163（62 aa） Fragment：UNP residues 102-163 Chain C 102–163（62 aa） Fragment：UNP residues 102-163 Chain D 102–163（62 aa） Fragment：UNP residues 102-163	Mutation：C143A Mutation：C143A Mutation：C143A Mutation：C143A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；20% v/v 2-Propanol, 0.1 M Tris pH 8.0, 5% w/v Polyethylene glycol 8,000	Resolution 2.20 Å R-free 0.281
8Z22 Crystal structure of the liprin-alpha2/RIM1 complex Deposited 2024-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 300–404（105 aa） Chain D 300–404（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；28% V/V 2-Propanol; 0.1M BIS-TRIS pH 6.5; 3% V/V Polyethylene glycol 200	Resolution 2.75 Å R-free 0.234

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LIPA2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 7–36； UniProt 642–671 Author chain D； PDBConstruct 7–36； UniProt 642–671

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	6iuh
Deposition date deposition_date	2018-11-28
Structure title title	Crystal structure of GIT1 PBD domain in complex with Liprin-alpha2
Keywords keywords	Complex, PROTEIN BINDING; PROTEIN BINDING
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	24.09 Å
Radius of gyration Rg (electron density) rg_electron	23.44 Å
Forward intensity I(0) i0	20867200.00
Molecular weight molecular_weight	34506.0 kDa
Excluded volume excluded_volume	43028 Å³
Envelope volume envelope_volume	54267 Å³
Hydration-shell volume shell_volume	20031 Å³
Envelope diameter envelope_diameter	83.1 Å
Shell Rg shell_rg	29.26 Å
Envelope Rg envelope_rg	23.41 Å
Shape Rg shape_rg	23.40 Å
Total Rg total_rg	24.28 Å
Total atoms total_atoms	2397
Residues n_residues	310
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	82.6 Å
Rg (real space) rg_real	24.16 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	2.0870e+07
I(0) uncertainty (real space) i0_real_error	2.8600e+05
Rg (reciprocal space) rg_reciprocal	24.15 Å
I(0) (reciprocal space) i0_reciprocal	20870000.0000
Solution quality estimate total_estimate	0.8699
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.370
Kurtosis Kurtosis kurtosis	-0.443
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7012000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.827; Smooth: 0.984

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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	ARF GTPase-activating protein GIT1
Molecular weight formula_weight	14692.9 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	2582

GPGSEFDPGLPSTEDVILKTEQVTKNIQELLRAAQEFKHDSFVPCSEKIHLAVTEMASLFPKRPALEPVRSSLRLLNASAYRLQSECRKTVPPEPGAPVDFQLLTQQVIQCAYDIAKAAKQLVTITTREKKQ

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Liprin-alpha-2
Molecular weight formula_weight	4032.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GPGSEFGHSDAQTLAMMLQEQLDAINKEIRLIQEEK

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 3 Entity 3 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6iuhA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

Domain ID domain_id	6iuhB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

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8. Citations (1)

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Unit-cell length a length_a	88.200 Å
Unit-cell length b length_b	38.617 Å
Unit-cell length c length_c	99.134 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	1.800 Å
Low-resolution limit resolution_low	49.567 Å
R factor r_factor	0.2285
R_work r_work	0.2266
R_free r_free	0.2668

fit	/app/data/saxs_computation/iu/6iuh/6iuh.fit
pddf	/app/data/pr_computation/iu/6iuh/6iuh.pr.out
profile	/app/data/saxs_computation/iu/6iuh/6iuh.dat

Crystal structure of GIT1 PBD domain in complex with Liprin-alpha2

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

ARF GTPase-activating protein GIT1

State in the Current Structure

Other States of the Same Protein in the Database

Liprin-alpha-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

6. Entities and Polymers Entities & Polymers (4)

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 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)