5TRU: First-in-class checkpoint inhibitor Ipilimumab

Structure of the first-in-class checkpoint inhibitor Ipilimumab bound to human CTLA-4. Determined by X-ray diffraction at 3.0 Å resolution. Released 10 May 2017.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,036
Mol. weight: 120.69 kDa
Released: 10 May 2017

Explore 5TRU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TRU contains 39 α-helices and 113 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain c: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	25
β-strand	10-12	3	14
α-helix	13-14	2
β-strand	19-26	8	25
β-strand	33-42	10	14
β-strand	45-55	11	14
β-strand	61-62	2	14
β-strand	68	1	25
β-strand	71-73	3	25
β-strand	76-81	6	25
β-strand	90-100	11	14
α-helix	104	1
β-strand	105-108	4	14
β-strand	112-115	4	14

Chain C: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	26
β-strand	10-12	3	3
α-helix	13-14	2
β-strand	19-26	8	26
β-strand	33-42	10	3
β-strand	45-55	11	3
α-helix	59-60	2
β-strand	68-69	2	26
β-strand	72	1	26
β-strand	76-81	6	26
α-helix	86-88	3
β-strand	90-100	11	3
α-helix	104	1
β-strand	105-108	4	3
β-strand	112-115	4	3

Chain h: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	11-12	2	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	34-39	6	20
β-strand	46-51	6	20
β-strand	58-60	3	20
β-strand	68-73	6	18
α-helix	74-76	3
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-99	8	20
β-strand	105-108	4	20
β-strand	112-114	3	20
β-strand	115-116	2	19
β-strand	122	1	21
α-helix	123-124	2
β-strand	125-129	5	22
α-helix	130-132	3
β-strand	141-150	10	22
β-strand	151	1	21
β-strand	156-159	4	23
α-helix	160-162	3
β-strand	164	1	23
β-strand	168-170	3	22
α-helix	171-173	3
β-strand	174-175	2	22
β-strand	181-189	9	22
β-strand	194	1	24
β-strand	197	1	24
β-strand	199-205	7	23
β-strand	210-216	7	23

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	58-60	3	8
α-helix	62-64	3
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-99	8	8
α-helix	100	1
β-strand	105-108	4	8
β-strand	113-116	4	8
β-strand	122	1	9
α-helix	123-124	2
β-strand	125-129	5	10
α-helix	130-132	3
β-strand	141-150	10	10
β-strand	151	1	9
β-strand	156-159	4	11
β-strand	169-170	2	10
α-helix	171-173	3
β-strand	174-175	2	10
β-strand	181-189	9	10
α-helix	192-194	3
β-strand	199-205	7	11
β-strand	210-216	7	11

Chain l: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
α-helix	30-32	3
β-strand	34-39	6	13
β-strand	46-50	5	13
β-strand	54-55	2	13
α-helix	56	1
β-strand	63-68	6	12
β-strand	71-76	6	12
α-helix	81-83	3
β-strand	86-91	6	13
β-strand	94	1	14
α-helix	97	1
β-strand	98-99	2	13
β-strand	103-107	5	13
β-strand	112	1	15
α-helix	113-114	2
β-strand	115-119	5	16
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	16
β-strand	141	1	15
β-strand	146-151	6	17
β-strand	155	1	17
β-strand	160-164	5	16
α-helix	165-168	4
β-strand	174-183	10	16
α-helix	184-187	4
β-strand	192-198	7	17
β-strand	206-211	6	17

Chain L: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	34-39	6	2
β-strand	46-50	5	2
β-strand	54-55	2	2
α-helix	56	1
β-strand	63-68	6	1
β-strand	71-76	6	1
α-helix	81-83	3
β-strand	86-91	6	2
β-strand	94	1	3
α-helix	97	1
β-strand	98-99	2	2
β-strand	103-107	5	2
β-strand	112	1	4
α-helix	113-114	2
β-strand	115-119	5	5
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	5
β-strand	141	1	4
β-strand	146-151	6	6
β-strand	154-155	2	6
α-helix	156	1
β-strand	160-164	5	5
α-helix	165-168	4
β-strand	174-183	10	5
α-helix	184-187	4
β-strand	192-198	7	6
β-strand	206-211	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ipilimumab Fab light chain	L, l	protein	215	Homo sapiens
Ipilimumab Fab heavy chain	H, h	protein	225	Homo sapiens
Cytotoxic T-lymphocyte protein 4	C, c	protein	118	Homo sapiens	P16410 (AlphaFold model)

Sequence of entity 1 (L, l), FASTA

>5TRU_1 Ipilimumab Fab light chain (chains L, l)
EIVLTQSPGTLSLSPGERATLSCRASQSVGSSYLAWYQQKPGQAPRLLIYGAFSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H, h), FASTA

>5TRU_2 Ipilimumab Fab heavy chain (chains H, h)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYTMHWVRQAPGKGLEWVTFISYDGNNKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARTGWLGPFDYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Sequence of entity 3 (C, c), FASTA

>5TRU_3 Cytotoxic T-lymphocyte protein 4 (chains C, c)
AMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNELT
FLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDP

Primary citation

Structural basis for cancer immunotherapy by the first-in-class checkpoint inhibitor ipilimumab. Ramagopal, U.A., Liu, W., Garrett-Thomson, S.C. et al. Proc Natl Acad Sci U S A (2017) 114:E4223-E4232. DOI 10.1073/pnas.1617941114 · PubMed

Other PDB entries of the same protein (UniProt P16410 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7CIO 1.1 Å, Molecular interactions of cytoplasmic region of CTLA-4 with SH2 domains of PI3-kinase
9DQ3 1.64 Å, Crystal structure of engineered Ipilimumab (mipi.4) Fab in complex with human CTLA-4
3OSK 1.8 Å, Crystal structure of human CTLA-4 apo homodimer
5GGV 2.0 Å, CTLA-4 in complex with tremelimumab Fab
3BX7 2.1 Å, Engineered Human Lipocalin 2 (LCN2) in Complex with the Extracellular Domain of Human…
7ELX 2.14 Å, The crystal structure of CTLA-4 and Fab
7DV4 2.38 Å, Crystal structure of anti-CTLA-4 VH domain in complex with human CTLA-4
7SU0 2.41 Å, Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.105 in complex with…
7SU1 2.53 Å, Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.106 in complex with…
2X44 2.6 Å, Structure of a strand-swapped dimeric form of CTLA-4
6RP8 2.6 Å, Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution
8GAB 2.72 Å, Crystal structure of CTLA-4 in complex with a high affinity CTLA-4 binder

Browse structure collections

About this viewer

MolViewer shows 5TRU directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.