6RP8: Ipilimumab Fab

Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution. Determined by X-ray diffraction at 2.6 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,177
Mol. weight: 120.69 kDa
Released: 8 Jul 2020

Explore 6RP8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RP8 contains 37 α-helices and 108 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: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	25
β-strand	10-13	4	9
β-strand	19-25	7	25
β-strand	33-42	10	9
β-strand	45-54	10	9
β-strand	61-63	3	9
β-strand	68-73	6	25
β-strand	76-81	6	25
β-strand	91-100	10	9
α-helix	104	1
β-strand	105-108	4	9
β-strand	112-116	5	9

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	24
β-strand	10-13	4	20
β-strand	19-26	8	24
β-strand	33-42	10	20
β-strand	45-55	11	20
β-strand	61-64	4	24
β-strand	68-73	6	24
β-strand	76-81	6	24
α-helix	86-88	3
β-strand	90-100	11	20
α-helix	104	1
β-strand	105-108	4	20
β-strand	112-116	5	20

Chain h: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
α-helix	100	1
β-strand	105-108	4	2
β-strand	112-116	5	2
β-strand	122	1	3
α-helix	123-124	2
β-strand	125-129	5	4
β-strand	141-150	10	4
β-strand	151	1	3
β-strand	156-159	4	5
α-helix	160-162	3
β-strand	168-170	3	4
α-helix	171-173	3
β-strand	174-175	2	4
β-strand	181-189	9	4
α-helix	191-193	3
β-strand	194	1	6
β-strand	197	1	6
β-strand	200-205	6	5
α-helix	206-208	3
β-strand	210-215	6	5

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-12	3	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	45-51	7	14
β-strand	58-60	3	14
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-99	8	14
α-helix	100	1
β-strand	105-108	4	14
β-strand	112-116	5	14
β-strand	122	1	15
α-helix	123-124	2
β-strand	125-129	5	16
β-strand	141-150	10	16
β-strand	151	1	15
β-strand	156-159	4	17
α-helix	160-162	3
β-strand	168-170	3	16
α-helix	171-173	3
β-strand	174-175	2	16
β-strand	181-189	9	16
α-helix	191-193	3
β-strand	199-205	7	17
α-helix	206-208	3
β-strand	210-216	7	17

Chain l: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-29	11	7
α-helix	31-33	3
β-strand	34-39	6	8
β-strand	46-50	5	8
β-strand	54-55	2	8
β-strand	63-76	14	7
α-helix	81-83	3
β-strand	86-91	6	8
β-strand	94	1	9
α-helix	97	1
β-strand	98-99	2	8
β-strand	103-107	5	8
α-helix	108	1
β-strand	112	1	10
α-helix	113-114	2
β-strand	115-119	5	11
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	11
β-strand	141	1	10
β-strand	146-151	6	12
β-strand	154-155	2	12
β-strand	160-164	5	11
α-helix	165-168	4
β-strand	174-183	10	11
α-helix	184-187	4
β-strand	193-198	6	12
β-strand	206-210	5	12

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-13	4	19
β-strand	19-29	11	18
α-helix	31-33	3
β-strand	34-39	6	19
β-strand	46-49	4	19
β-strand	55	1	19
β-strand	63-76	14	18
α-helix	81-83	3
β-strand	86-91	6	19
β-strand	94	1	20
α-helix	97	1
β-strand	98-99	2	19
β-strand	103-107	5	19
α-helix	108	1
β-strand	112	1	21
α-helix	113-114	2
β-strand	115-119	5	22
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	22
β-strand	141	1	21
β-strand	145-151	7	23
β-strand	154-155	2	23
β-strand	160-164	5	22
α-helix	165-168	4
β-strand	174-183	10	22
α-helix	184-187	4
β-strand	193-199	7	23
β-strand	206-210	5	23

Molecules and chains

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

Sequence of entity 1 (H, h), FASTA

>6RP8_1 Antibody Ipilimumab heavy chain (chains H, h)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYTMHWVRQAPGKGLEWVTFISYDGNNKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARTGWLGPFDYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Sequence of entity 2 (L, l), FASTA

>6RP8_2 Antibody Ipilimumab light chain (chains L, l)
EIVLTQSPGTLSLSPGERATLSCRASQSVGSSYLAWYQQKPGQAPRLLIYGAFSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, c), FASTA

>6RP8_3 Cytotoxic T-lymphocyte protein 4 (chains C, c)
AMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNELT
FLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDP

Primary citation

Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution. Zhang, F., Zhou, A. To be published.

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
8GAB 2.72 Å, Crystal structure of CTLA-4 in complex with a high affinity CTLA-4 binder
1I8L 3.0 Å, Human B7-1/CTLA-4 co-stimulatory complex

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