SAXSdb — 2gdc

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

Vinculin

Gallus gallus

UniProt P12003

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 1–265	Fragment：VD1 domain (RESIDUES 0-265)	Invasin ipaA × 1 （P18010）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM HEPES, 10% 2-propanol, 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.74 Å R-free 0.294

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 2GDC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QKR Crystal structure of the vinculin tail and a pathway for activation Deposited 1999-08-04	Different construct 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 A 878–1065（188 aa） Fragment：C-TERMINAL DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；25% (W/V) PEG 2000, 0.2 M (NH4)2SO4, 0.1 M CH3COO PH 5.0	Resolution 1.80 Å R-free 0.248
1QKR Crystal structure of the vinculin tail and a pathway for activation Deposited 1999-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 878–1065（188 aa） Fragment：C-TERMINAL DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；25% (W/V) PEG 2000, 0.2 M (NH4)2SO4, 0.1 M CH3COO PH 5.0	Resolution 1.80 Å R-free 0.248
1ST6 Crystal structure of a cytoskeletal protein Deposited 2004-03-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1065（1065 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；303 K；ammonium sulphate, cacodylic acid, dtt, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K	Resolution 3.10 Å R-free 0.357
1T01 Vinculin complexed with the VBS1 helix from talin Deposited 2004-04-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–254（254 aa） Fragment：vinculin head	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；293 K；30%PEG 5000, 0.1M MES, 0.2M Ammonium Sulphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.50	Resolution 2.06 Å R-free 0.303
1U6H Vinculin head (0-258) in complex with the talin vinculin binding site 2 (849-879) Deposited 2004-07-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 0–258（259 aa） Fragment：Residues 0-258	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 8000, Tris-HCl, magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.38 Å R-free 0.322
1XWJ Vinculin head (1-258) in complex with the talin vinculin binding site 3 (1945-1969) Deposited 2004-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–258（258 aa） Fragment：residues -21-258	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1M NaH2PO4, 1M K2HPO4, 0.1M CAPS, pH 10.9, 3% Hexanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.281
1ZVZ Vinculin Head (0-258) in Complex with the Talin Rod Residue 820-844 Deposited 2005-06-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–258（258 aa） Fragment：Residues 0-258	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.276
1ZW2 Vinculin Head (0-258) in Complex with the Talin Rod residues 2345-2369 Deposited 2005-06-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–258（258 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100mM Tris, pH 7.0, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.295
1ZW3 Vinculin Head (0-258) in Complex with the Talin Rod residues 1630-1652 Deposited 2005-06-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–258（258 aa） Fragment：Residues 0-258	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；293 K；1.2M NaH2PO4/0.8M K2HPO4, 100mM CAPS, pH 10.5, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.30 Å R-free 0.307
3JBI MDFF model of the vinculin tail domain bound to F-actin Deposited 2015-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 879–1130（252 aa） Fragment：tail domain (UNP residues 879-1130)	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM imidazole；pH 7；50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM imidazole cryo-EM vitrification conditions 3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar Vt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of Vt applied. After 60 seconds, 3 microliters of solution was removed, then the grid was blotted for 2 seconds before plunging.；Cryogen ETHANE；3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar Vt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of Vt applied. After 60 seconds, 3 microliters of solution was removed, then the grid was blotted for 2 seconds before plunging into liquid ethane (LEICA EM GP).	Resolution 8.50 Å
3ZDL Vinculin head (1-258) in complex with a RIAM fragment Deposited 2012-11-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–259（259 aa） Fragment：VD1 DOMAIN, RESIDUES 1-259	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 1.2M AMMONIUM SULPHATE, 0.05M TRI-SODIUM CITRATE, 3% ISOPROPANOL	Resolution 2.30 Å R-free 0.230
4E17 Alpha-E-catenin is an autoinhibited molecule that co-activates vinculin Deposited 2012-03-05	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–259（259 aa） Fragment：D1 domain (UNP residues 1-259)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；283 K；20% PEG8000, 100 mM MES, pH 6.8, 3 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.30 Å R-free 0.240
4E18 Alpha-E-catenin is an autoinhibited molecule that co-activates vinculin Deposited 2012-03-05	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–259（259 aa） Fragment：D1 domain (UNP residues 1-259)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；22% PEG3350, 100 mM bis-tris-propane, pH 8.0, 100 mM sodium nitrate, 3 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.273
6FQ4 Structure of Chlamydial virulence factor TarP and vinculin head domain Deposited 2018-02-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–259（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1 M sodium citrate tribasic dehydrate pH 5.6, 20% 2-propanol	Resolution 2.89 Å R-free 0.346
6NR7 Rerefinement of chicken vinculin Deposited 2019-01-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1066（1066 aa）	Not recorded	SO4 SULFATE ION × 2 KYG (1R,2R,3S,4R,5R,6S)-4-{[(S)-[(2S)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-3,5,6-trihydroxycyclohexane-1,2-diyl bis[dihydrogen (phosphate)] × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；303 K；ammonium sulphate, cacodylic acid, dtt, pH 6.5	Resolution 3.00 Å R-free 0.315

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VINC_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–266； UniProt 1–265

Invasin ipaA

Shigella flexneri

UniProt P18010

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 B； UniProt 564–584	Fragment：C-terminal fragment (RESIDUES 560-633)	Vinculin × 1 （P12003）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM HEPES, 10% 2-propanol, 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.74 Å R-free 0.294

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 2GDC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2HSQ Human vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site 2 (residues 565-587) Deposited 2006-07-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 565–587（23 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.97 Å R-free 0.316
2HSQ Human vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site 2 (residues 565-587) Deposited 2006-07-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	Chain B 565–587（23 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.97 Å R-free 0.316
2HSQ Human vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site 2 (residues 565-587) Deposited 2006-07-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 565–587（23 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.97 Å R-free 0.316
2IBF Human vinculin's head domain (Vh1, residues 1-258) in complex with two vinculin binding sites of Shigella flexneri's IpaA (residues 565-587) Deposited 2006-09-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 563–587（25 aa） Fragment：Vinculin binding sites: Residues 565-587 Chain D 563–587（25 aa） Fragment：Vinculin binding sites: Residues 565-587	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.270
3RF3 Shigella IpaA-VBS3 in complex with human vinculin Deposited 2011-04-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 488–512（25 aa） Fragment：unp residues 488-512	Not recorded	CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；0.1 M sodium citrate, 20% PEG 3350, 0.1 M cacodylate, pH 7.2, VAPOR DIFFUSION, temperature 298K	Resolution 1.61 Å R-free 0.195
3RF3 Shigella IpaA-VBS3 in complex with human vinculin Deposited 2011-04-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 488–512（25 aa） Fragment：unp residues 488-512	Not recorded	CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；0.1 M sodium citrate, 20% PEG 3350, 0.1 M cacodylate, pH 7.2, VAPOR DIFFUSION, temperature 298K	Resolution 1.61 Å R-free 0.195
3RF3 Shigella IpaA-VBS3 in complex with human vinculin Deposited 2011-04-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 488–512（25 aa） Fragment：unp residues 488-512 Chain D 488–512（25 aa） Fragment：unp residues 488-512	Not recorded	CAC CACODYLATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；0.1 M sodium citrate, 20% PEG 3350, 0.1 M cacodylate, pH 7.2, VAPOR DIFFUSION, temperature 298K	Resolution 1.61 Å R-free 0.195
5NL1 Shigella IpaA-VBS3/TBS in complex with the Talin VBS1 domain 488-512 Deposited 2017-04-03	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 H 488–512（25 aa） Fragment：UNP residues 488-512 Chain I 488–512（25 aa） Fragment：UNP residues 488-512	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；292 K；0.2 M ammonium sulfate 0.1 M sodium acetate pH 4.6 30 % PEG 4000	Resolution 2.50 Å R-free 0.228
5NL1 Shigella IpaA-VBS3/TBS in complex with the Talin VBS1 domain 488-512 Deposited 2017-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain J 488–512（25 aa） Fragment：UNP residues 488-512 Chain L 488–512（25 aa） Fragment：UNP residues 488-512	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；292 K；0.2 M ammonium sulfate 0.1 M sodium acetate pH 4.6 30 % PEG 4000	Resolution 2.50 Å R-free 0.228
5NL1 Shigella IpaA-VBS3/TBS in complex with the Talin VBS1 domain 488-512 Deposited 2017-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 488–512（25 aa） Fragment：UNP residues 488-512 Chain K 488–512（25 aa） Fragment：UNP residues 488-512	Not recorded	CL CHLORIDE ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；292 K；0.2 M ammonium sulfate 0.1 M sodium acetate pH 4.6 30 % PEG 4000	Resolution 2.50 Å R-free 0.228

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

View Construct and Data Evidence

UniProt name	IPAA_SHIFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–21； UniProt 564–584

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	2gdc
Deposition date deposition_date	2006-03-15
Structure title title	Structure of Vinculin VD1 / IpaA560-633 complex
Keywords keywords	IpaA-Vinculin complex, Shigella flexneri, Helical bundle conversion, CELL INVASION; CELL INVASION
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	26.23 Å
Radius of gyration Rg (electron density) rg_electron	26.50 Å
Forward intensity I(0) i0	13582300.00
Molecular weight molecular_weight	28459.0 kDa
Excluded volume excluded_volume	36025 Å³
Envelope volume envelope_volume	45635 Å³
Hydration-shell volume shell_volume	16982 Å³
Envelope diameter envelope_diameter	102.3 Å
Shell Rg shell_rg	28.68 Å
Envelope Rg envelope_rg	26.83 Å
Shape Rg shape_rg	26.51 Å
Total Rg total_rg	26.76 Å
Total atoms total_atoms	1992
Residues n_residues	259
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	98.7 Å
Rg (real space) rg_real	26.78 Å
Rg uncertainty (real space) rg_real_error	1.20 Å
I(0) (real space) i0_real	1.3580e+07
I(0) uncertainty (real space) i0_real_error	2.2590e+05
Rg (reciprocal space) rg_reciprocal	26.61 Å
I(0) (reciprocal space) i0_reciprocal	13580000.0000
Solution quality estimate total_estimate	0.7168
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.7 Å
Skewness Skewness skewness	0.736
Kurtosis Kurtosis kurtosis	0.001
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3056000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.407; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.132; Smooth: 0.962

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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	Vinculin
Molecular weight formula_weight	29788.4 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	2006

MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVSAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVRAAQMLQADPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNTKSQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAWASKDTEAM

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Invasin ipaA
Molecular weight formula_weight	2099.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XXIYXXAKXVXXXLSKVLXXI

来源 Source

来源生物 organism	Shigella flexneri
NCBI Class编号 ncbi_taxonomy_id	623
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2gdca1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.9 — alpha-catenin/vinculin-like
Family Family family	a.24.9.1 — alpha-catenin/vinculin

Domain ID domain_id	d2gdca2
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.9 — alpha-catenin/vinculin-like
Family Family family	a.24.9.1 — alpha-catenin/vinculin

CATH v4.4 (2 domains)

Domain ID domain_id	2gdcA01
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	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	2gdcA02
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	230 — Alpha-catenin/vinculin-like

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8. Citations (1)

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Unit-cell length a length_a	52.684 Å
Unit-cell length b length_b	68.326 Å
Unit-cell length c length_c	96.521 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.740 Å
Low-resolution limit resolution_low	15.180 Å
R factor r_factor	0.2497
R_work r_work	0.2470
R_free r_free	0.2940

fit	/app/data/saxs_computation/gd/2gdc/2gdc.fit
pddf	/app/data/pr_computation/gd/2gdc/2gdc.pr.out
profile	/app/data/saxs_computation/gd/2gdc/2gdc.dat

Structure of Vinculin VD1 / IpaA560-633 complex

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

Vinculin

State in the Current Structure

Other States of the Same Protein in the Database

Invasin ipaA

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 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)