5tru

Structure of the first-in-class checkpoint inhibitor Ipilimumab bound to human CTLA-4

Method: X-RAY DIFFRACTION D_max: 128.8 Å Quality: GOOD

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

Cytotoxic T-lymphocyte protein 4

Homo sapiens

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 37–154	Fragment：UNP residues 37-154	Ipilimumab Fab light chain × 1 Ipilimumab Fab heavy chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；291 K；0.1M ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG 1500	Resolution 3.00 Å R-free 0.268
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain c； UniProt 37–154	Fragment：UNP residues 37-154	Ipilimumab Fab light chain × 1 Ipilimumab Fab heavy chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；291 K；0.1M ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG 1500	Resolution 3.00 Å R-free 0.268

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 5TRU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AH1 CTLA-4, NMR, 20 STRUCTURES Deposited 1997-04-11	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 37–161（125 aa） Fragment：EXTRACELLULAR N-TERMINAL IMMUNOGLOBULIN V-LIKE	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K	Resolution not provided
1H6E MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH CTLA-4 INTERNALIZATION PEPTIDE TTGVYVKMPPT Deposited 2001-06-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 197–207（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROPS CONTAINING A 1:1 MIXTURE OF COMPLEX SOLUTION 6MG/ML PROTEIN AND 1MM 11MER PEPTIDE SOLUTION IN 20MM HEPES PH7.5, 1MM DTT AND RESERVOIR BUFFER 1.4-2.4M SODIUM CHLORIDE, 0.1M MES PH6.2-7.0, 0.4M NA/K PHOSPHATE, 15% GLYCEROL, pH 7.00	Resolution 3.60 Å R-free 0.317
1I85 CRYSTAL STRUCTURE OF THE CTLA-4/B7-2 COMPLEX Deposited 2001-03-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 36–161（126 aa） Fragment：EXTRACELLULAR DOMAIN Chain D 36–161（126 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG20K, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.300
1I8L HUMAN B7-1/CTLA-4 CO-STIMULATORY COMPLEX Deposited 2001-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 36–161（126 aa） Fragment：EXTRACELLULAR DOMAIN, RESIDUES 36-161	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MAN alpha-D-mannopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；16% PEG 8000, 0.1M CACODYLATE, PH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.00 Å R-free 0.257
1I8L HUMAN B7-1/CTLA-4 CO-STIMULATORY COMPLEX Deposited 2001-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 36–161（126 aa） Fragment：EXTRACELLULAR DOMAIN, RESIDUES 36-161	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MAN alpha-D-mannopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；16% PEG 8000, 0.1M CACODYLATE, PH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.00 Å R-free 0.257
2X44 Structure of a strand-swapped dimeric form of CTLA-4 Deposited 2010-01-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 36–161（126 aa） Fragment：RESIDUES 36-161	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.02 M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 22 % W/V POLYACRYLIC ACID 5100 SODIUM SALT, 0.4 M NDSB-256 (OR 6 % 1,6-DIAMINOHEXANE).	Resolution 2.60 Å R-free 0.245
3BX7 Engineered Human Lipocalin 2 (LCN2) in Complex with the Extracellular Domain of Human CTLA-4 Deposited 2008-01-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 38–161（124 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293.15 K；1.4 M Na-malonate, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.10 Å R-free 0.226
3OSK Crystal structure of human CTLA-4 apo homodimer Deposited 2010-09-09	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 36–161（126 aa） Fragment：Extracellular domain, UNP residues 36-161 Chain B 36–161（126 aa） Fragment：Extracellular domain, UNP residues 36-161	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；25% Polyethylene glycol 3350 (w/v), 100mM bis-Tris pH 5.5, 200mM ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.275
5GGV CTLA-4 in complex with tremelimumab Fab Deposited 2016-06-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Y 36–161（126 aa） Fragment：UNP residues 36-161	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate tribasic dihydrate, pH 5.6, 12% PEG4,000, 100 mM NaCl	Resolution 2.00 Å R-free 0.214
5XJ3 Complex structure of ipilimumab-scFv and CTLA-4 Deposited 2017-04-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain L 36–161（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；291 K；100 mM BICINE, 10% PEG 20000, 2% 1,4-Dioxane, pH 9.0.	Resolution 3.20 Å R-free 0.264
5XJ3 Complex structure of ipilimumab-scFv and CTLA-4 Deposited 2017-04-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 36–161（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；291 K；100 mM BICINE, 10% PEG 20000, 2% 1,4-Dioxane, pH 9.0.	Resolution 3.20 Å R-free 0.264
5XJ3 Complex structure of ipilimumab-scFv and CTLA-4 Deposited 2017-04-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 36–161（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；291 K；100 mM BICINE, 10% PEG 20000, 2% 1,4-Dioxane, pH 9.0.	Resolution 3.20 Å R-free 0.264
5XJ3 Complex structure of ipilimumab-scFv and CTLA-4 Deposited 2017-04-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 36–161（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；291 K；100 mM BICINE, 10% PEG 20000, 2% 1,4-Dioxane, pH 9.0.	Resolution 3.20 Å R-free 0.264
6RP8 Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution Deposited 2019-05-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain c 37–154（118 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG4000, pH6	Resolution 2.60 Å R-free 0.267
6RP8 Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution Deposited 2019-05-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 37–154（118 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG4000, pH6	Resolution 2.60 Å R-free 0.267
6RPJ A Non-blocking anti-CTLA-4 Nanobody complexed with CTLA-4 Deposited 2019-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 37–156（120 aa） Chain G 37–156（120 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400	Resolution 3.25 Å R-free 0.262
6RPJ A Non-blocking anti-CTLA-4 Nanobody complexed with CTLA-4 Deposited 2019-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 37–156（120 aa） Chain E 37–156（120 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400	Resolution 3.25 Å R-free 0.262
6RQM A blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4 Deposited 2019-05-16	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 37–161（125 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG400,	Resolution 3.00 Å R-free 0.313
6XY2 Crystal structure of CTLA-4 complexed with the Fab of HL32 antibody Deposited 2020-01-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 38–160（123 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 6.5；293 K；1M Li2SO4, 1.5M NH4SO4, 0.1M Sodium citrate	Resolution 3.05 Å R-free 0.292
7CIO Molecular interactions of cytoplasmic region of CTLA-4 with SH2 domains of PI3-kinase Deposited 2020-07-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 199–206（8 aa）	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, HANGING DROP；pH 4.6；293 K；0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate pH 4.6, 30% PEG 4000	Resolution 1.10 Å R-free 0.179
7DV4 Crystal structure of anti-CTLA-4 VH domain in complex with human CTLA-4 Deposited 2021-01-12	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 A 36–153（118 aa） Chain G 36–153（118 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM sodium citrate, 10% (w/v) PEG 6000, pH 5.0	Resolution 2.38 Å R-free 0.258
7DV4 Crystal structure of anti-CTLA-4 VH domain in complex with human CTLA-4 Deposited 2021-01-12	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 C 36–153（118 aa） Chain E 36–153（118 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM sodium citrate, 10% (w/v) PEG 6000, pH 5.0	Resolution 2.38 Å R-free 0.258
7ELX The crystal structure of CTLA-4 and Fab Deposited 2021-04-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 36–161（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；PEG8000 10%, 0.1M Na Citrate 0.1M (NH4)2SO4	Resolution 2.14 Å R-free 0.217
7ELX The crystal structure of CTLA-4 and Fab Deposited 2021-04-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain c 36–161（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；PEG8000 10%, 0.1M Na Citrate 0.1M (NH4)2SO4	Resolution 2.14 Å R-free 0.217
7SU0 Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.105 in complex with CTLA-4 Deposited 2021-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 36–153（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium citrate dibasic, 20% w/v PEG 1,000, pH 5.2	Resolution 2.41 Å R-free 0.264
7SU0 Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.105 in complex with CTLA-4 Deposited 2021-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 36–153（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FLC CITRATE ANION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium citrate dibasic, 20% w/v PEG 1,000, pH 5.2	Resolution 2.41 Å R-free 0.264
7SU1 Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.106 in complex with CTLA-4 Deposited 2021-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 36–153（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium citrate tribasic dehydrate, 22% PEG 3,350	Resolution 2.53 Å R-free 0.251
8GAB Crystal structure of CTLA-4 in complex with a high affinity CTLA-4 binder Deposited 2023-02-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 36–161（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；22% (w/v) PEG 3350 and 0.2 M KCl	Resolution 2.72 Å R-free 0.292
8GAB Crystal structure of CTLA-4 in complex with a high affinity CTLA-4 binder Deposited 2023-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 36–161（126 aa）	Not recorded	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；22% (w/v) PEG 3350 and 0.2 M KCl	Resolution 2.72 Å R-free 0.292
8HIT Crystal structure of anti-CTLA-4 humanized IgG1 MAb--JS007 in complex with human CTLA-4 Deposited 2022-11-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 35–154（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100mM Tris, pH 8.5, 30% w/v PEG 4000	Resolution 3.20 Å R-free 0.298
9DQ3 Crystal structure of engineered Ipilimumab (mipi.4) Fab in complex with human CTLA-4 Deposited 2024-09-23	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 36–153（118 aa） Fragment：Extracellular domain of human CTLA-4 with hexahistidine tag	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；300 K；0.18 M calcium acetate hydrate, 22.5% w/v PEG3350	Resolution 1.64 Å R-free 0.268

21 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CTLA4_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–118； UniProt 37–154 Author chain c； PDBConstruct 1–118； UniProt 37–154

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5tru
Deposition date deposition_date	2016-10-27
Structure title title	Structure of the first-in-class checkpoint inhibitor Ipilimumab bound to human CTLA-4
Keywords keywords	antibody, complex, Fab, IMMUNE SYSTEM; IMMUNE SYSTEM
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	42.53 Å
Radius of gyration Rg (electron density) rg_electron	42.15 Å
Forward intensity I(0) i0	198468000.00
Molecular weight molecular_weight	114070.0 kDa
Excluded volume excluded_volume	142020 Å³
Envelope volume envelope_volume	206500 Å³
Hydration-shell volume shell_volume	40459 Å³
Envelope diameter envelope_diameter	132.5 Å
Shell Rg shell_rg	48.01 Å
Envelope Rg envelope_rg	40.90 Å
Shape Rg shape_rg	42.13 Å
Total Rg total_rg	42.52 Å
Total atoms total_atoms	8036
Residues n_residues	1081
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	128.8 Å
Rg (real space) rg_real	42.57 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	1.9850e+08
I(0) uncertainty (real space) i0_real_error	3.5990e+06
Rg (reciprocal space) rg_reciprocal	42.53 Å
I(0) (reciprocal space) i0_reciprocal	198500000.0000
Solution quality estimate total_estimate	0.8459
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.8 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-0.901
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12810000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.184

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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	Ipilimumab Fab light chain
Molecular weight formula_weight	23477.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,l
Atom count atom_count	8036

EIVLTQSPGTLSLSPGERATLSCRASQSVGSSYLAWYQQKPGQAPRLLIYGAFSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Ipilimumab Fab heavy chain
Molecular weight formula_weight	24232.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,h

QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYTMHWVRQAPGKGLEWVTFISYDGNNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARTGWLGPFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Cytotoxic T-lymphocyte protein 4
Molecular weight formula_weight	12637.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNELTFLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDP

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

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5truc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5truh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5trul1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5trul2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (8 domains)

Domain ID domain_id	5truC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5truH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5truL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5truL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5truc00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5truh02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5trul01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5trul02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	95.844 Å
Unit-cell length b length_b	197.502 Å
Unit-cell length c length_c	148.117 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	34.910 Å
R factor r_factor	0.2067
R_work r_work	0.2035
R_free r_free	0.2677

fit	/app/data/saxs_computation/tr/5tru/5tru.fit
pddf	/app/data/pr_computation/tr/5tru/5tru.pr.out
profile	/app/data/saxs_computation/tr/5tru/5tru.dat

Structure of the first-in-class checkpoint inhibitor Ipilimumab bound to human CTLA-4

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

Cytotoxic T-lymphocyte protein 4

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 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)