2b5i

cytokine receptor complex

Method: X-RAY DIFFRACTION Dmax: 101.0 Å Quality: EXCELLENT

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

Interleukin-2

Homo sapiens

UniProt P60568

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 21–153 Not recorded Interleukin-2 receptor beta chain × 1 (P14784) Cytokine receptor common gamma chain × 1 (P31785) Interleukin-2 receptor alpha chain × 1 (P01589) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.1;293 K;29% Pentaerythritol Ethoxylate 15/4; 50 mM Ammonium Sulfate; 50 mM Bis Tris, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.30 Å R-free 0.269

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.

33 other PDB entries and 77 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–133; UniProt 21–153

Interleukin-2 receptor beta chain

Homo sapiens

UniProt P14784

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 27–240 Mutation:N3Q,N17Q,N45Q Interleukin-2 × 1 (P60568) Cytokine receptor common gamma chain × 1 (P31785) Interleukin-2 receptor alpha chain × 1 (P01589) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.1;293 K;29% Pentaerythritol Ethoxylate 15/4; 50 mM Ammonium Sulfate; 50 mM Bis Tris, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.30 Å R-free 0.269

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.

7 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL2RB_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–214; UniProt 27–240

Cytokine receptor common gamma chain

Homo sapiens

UniProt P31785

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 C; UniProt 56–254 Mutation:N53Q Interleukin-2 × 1 (P60568) Interleukin-2 receptor beta chain × 1 (P14784) Interleukin-2 receptor alpha chain × 1 (P01589) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.1;293 K;29% Pentaerythritol Ethoxylate 15/4; 50 mM Ammonium Sulfate; 50 mM Bis Tris, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.30 Å R-free 0.269

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.

13 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL2RG_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–199; UniProt 56–254

Interleukin-2 receptor alpha chain

Homo sapiens

UniProt P01589

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 D; UniProt 22–238 Mutation:N68Q Interleukin-2 × 1 (P60568) Interleukin-2 receptor beta chain × 1 (P14784) Cytokine receptor common gamma chain × 1 (P31785) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.1;293 K;29% Pentaerythritol Ethoxylate 15/4; 50 mM Ammonium Sulfate; 50 mM Bis Tris, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.30 Å R-free 0.269

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.

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL2RA_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–217; UniProt 22–238

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 2b5i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2b5i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2b5i
Deposition date deposition_date2005-09-28
Structure title titlecytokine receptor complex
Keywords keywordsfour-helix bundle, Fibronectin domain, CYTOKINE-CYTOKINE RECEPTOR COMPLEX; CYTOKINE/CYTOKINE RECEPTOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.61
Radius of gyration Rg (electron density) rg_electron30.69
Forward intensity I(0) i092393700.00
Molecular weight molecular_weight75289.0 kDa
Excluded volume excluded_volume93880 ų
Envelope volume envelope_volume123600 ų
Hydration-shell volume shell_volume34199 ų
Envelope diameter envelope_diameter107.1
Shell Rg shell_rg37.04
Envelope Rg envelope_rg30.93
Shape Rg shape_rg30.68
Total Rg total_rg31.30
Total atoms total_atoms5292
Residues n_residues629
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 dmax101.0
Rg (real space) rg_real31.55
Rg uncertainty (real space) rg_real_error0.77
I(0) (real space) i0_real9.2390e+07
I(0) uncertainty (real space) i0_real_error1.4480e+06
Rg (reciprocal space) rg_reciprocal31.58
I(0) (reciprocal space) i0_reciprocal92400000.0000
Solution quality estimate total_estimate0.9017
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.4
Skewness Skewness skewness0.209
Kurtosis Kurtosis kurtosis-0.508
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12680000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.897

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd2b5ia_
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.2 — Short-chain cytokines
Domain ID domain_idd2b5ib1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2b5ib2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2b5ic1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2b5ic2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2b5id1
Class classg — Small proteins
Fold Fold foldg.18 — Complement control module/SCR domain
Superfamily Superfamily superfamilyg.18.1 — Complement control module/SCR domain
Family Family familyg.18.1.1 — Complement control module/SCR domain
Domain ID domain_idd2b5id2
Class classg — Small proteins
Fold Fold foldg.18 — Complement control module/SCR domain
Superfamily Superfamily superfamilyg.18.1 — Complement control module/SCR domain
Family Family familyg.18.1.1 — Complement control module/SCR domain

CATH v4.4 (7 domains)

Domain ID domain_id2b5iA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10
Domain ID domain_id2b5iB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2b5iB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2b5iC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2b5iC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2b5iD01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology70 — Complement Module; domain 1
Homologous superfamily homologous superfamily10 — Complement Module, domain 1
Domain ID domain_id2b5iD02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily230

8. Citations (1)

9. Files and Curves (10)