2vc2

Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist L-739758

Method: X-RAY DIFFRACTION Dmax: 135.3 Å Quality: REASONABLE

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

INTEGRIN ALPHA-IIB

HOMO SAPIENS

UniProt P08514

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 32–483 Fragment:HEADPIECE, RESIDUES 32-483 INTEGRIN BETA-3 × 1 (P05106) MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN × 1 MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2 CA CALCIUM ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 180 2-(S)-[N-(3-PYRIDYLSULFONYL)AMINO]-3-[[2-CARBONYL-5-[2-(PIPERIDIN-4-YL)ETHYL]-THIENO[2,3-B]THIOPHENEYL]AMINO]-PROPIONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;10-12% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K Resolution 3.10 Å R-free 0.217

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.

76 other PDB entries and 116 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ITA2B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–452; UniProt 32–483

INTEGRIN BETA-3

HOMO SAPIENS

UniProt P05106

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 27–487 Fragment:HEADPIECE, RESIDUES 27-487 INTEGRIN ALPHA-IIB × 1 (P08514) MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN × 1 MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2 CA CALCIUM ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 180 2-(S)-[N-(3-PYRIDYLSULFONYL)AMINO]-3-[[2-CARBONYL-5-[2-(PIPERIDIN-4-YL)ETHYL]-THIENO[2,3-B]THIOPHENEYL]AMINO]-PROPIONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;10-12% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K Resolution 3.10 Å R-free 0.217

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.

124 other PDB entries and 176 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ITB3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–461; UniProt 27–487

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2vc2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2vc2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2vc2
Deposition date deposition_date2007-09-18
Structure title titleRe-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist L-739758
Keywords keywordsCELL ADHESION-IMMUNE SYSTEM COMPLEX, FIBRINOGEN BINDING, HOST-VIRUS INTERACTION, PYRROLIDONE CARBOXYLIC ACID, TRANSMEMBRANE; CELL ADHESION/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier52.00
Radius of gyration Rg (electron density) rg_electron52.66
Forward intensity I(0) i0349902000.00
Molecular weight molecular_weight150130.0 kDa
Excluded volume excluded_volume186480 ų
Envelope volume envelope_volume266190 ų
Hydration-shell volume shell_volume50648 ų
Envelope diameter envelope_diameter217.2
Shell Rg shell_rg43.06
Envelope Rg envelope_rg55.86
Shape Rg shape_rg52.52
Total Rg total_rg52.71
Total atoms total_atoms10537
Residues n_residues1342
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax135.3
Rg (real space) rg_real46.24
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real3.3070e+08
I(0) uncertainty (real space) i0_real_error5.7310e+06
Rg (reciprocal space) rg_reciprocal51.08
I(0) (reciprocal space) i0_reciprocal348900000.0000
Solution quality estimate total_estimate0.6601
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.1
Skewness Skewness skewness0.389
Kurtosis Kurtosis kurtosis-0.757
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.5723
Highest regularization parameter α highest_alpha16330000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.016; Oscil: 0.931; Stabil: 0.988; Sysdev: 0.000; Positv: 1.000; Valcen: 0.856; Smooth: 0.001

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (12)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2vc2a_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.8 — Integrin alpha N-terminal domain
Family Family familyb.69.8.1 — Integrin alpha N-terminal domain
Domain ID domain_idd2vc2h_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2vc2l1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd2vc2l2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (8 domains)

Domain ID domain_id2vc2A00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily130 — Integrin alpha, N-terminal
Domain ID domain_id2vc2B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1680 — ligand-binding face of the semaphorins, domain 2
Homologous superfamily homologous superfamily10 — ligand-binding face of the semaphorins, domain 2
Domain ID domain_id2vc2B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1510 — ntegrin, alpha v. Chain A, domain 3
Domain ID domain_id2vc2B03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily410 — von Willebrand factor, type A domain
Domain ID domain_id2vc2H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2vc2H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2vc2L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2vc2L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (2)

9. Files and Curves (10)