5XJ3: Complex structure of ipilimumab-scFv and CTLA-4

Complex structure of ipilimumab-scFv and CTLA-4. Determined by X-ray diffraction at 3.2 Å resolution. Released 25 Apr 2018.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 12
Atoms: 10,424
Mol. weight: 154.67 kDa
Released: 25 Apr 2018

Explore 5XJ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XJ3 contains 36 α-helices and 134 β-strands across 12 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 A: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	58-60	3	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	3
α-helix	100	1
β-strand	105-108	4	3
β-strand	112-114	3	3
β-strand	115-116	2	2

Chains B and K: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-13	4	5
β-strand	19-25	7	4
β-strand	34-39	6	5
β-strand	45-50	6	5
β-strand	54-55	2	5
α-helix	56	1
β-strand	63-67	5	4
β-strand	71-76	6	4
α-helix	81-83	3
β-strand	85-91	7	5
β-strand	94	1	6
α-helix	97	1
β-strand	98-99	2	5
β-strand	103-107	5	5

Chains C and F: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	40-41	2	7
β-strand	45-47	3	6
β-strand	54-60	7	7
β-strand	69-77	9	6
β-strand	80-87	8	6
α-helix	94-95	2
β-strand	103-108	6	7
β-strand	111-116	6	7
α-helix	121-123	3
β-strand	125-133	9	6
α-helix	139	1
β-strand	140-143	4	6
β-strand	147-150	4	6

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	58-60	3	9
β-strand	68-73	6	8
β-strand	78-83	6	8
β-strand	92-99	8	9
α-helix	100	1
β-strand	105-108	4	9
β-strand	112-116	5	9

Chain E: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	11
β-strand	19-25	7	10
β-strand	34-39	6	11
β-strand	46-50	5	11
β-strand	54-55	2	11
α-helix	56	1
β-strand	63-67	5	10
β-strand	71-76	6	10
α-helix	81-83	3
β-strand	85-91	7	11
β-strand	94	1	12
α-helix	97	1
β-strand	98-99	2	11
β-strand	103-107	5	11

Chain G: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	10-12	3	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	45-51	7	15
β-strand	58-60	3	15
β-strand	68-73	6	14
β-strand	78-83	6	14
β-strand	92-98	7	15
α-helix	99-100	2
β-strand	107-108	2	15
β-strand	112-116	5	15

Chain H: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-13	4	17
β-strand	19-25	7	16
β-strand	34-39	6	17
β-strand	45-49	5	17
α-helix	54	1
β-strand	55	1	17
α-helix	56	1
β-strand	63-67	5	16
β-strand	71-76	6	16
α-helix	81-83	3
β-strand	85-91	7	17
β-strand	94	1	18
α-helix	97	1
β-strand	98-99	2	17
β-strand	103-107	5	17

Chain I: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	40-41	2	19
β-strand	45-47	3	18
α-helix	48-49	2
β-strand	54-60	7	19
β-strand	69-75	7	18
β-strand	82-89	8	18
α-helix	94-95	2
β-strand	103-108	6	19
β-strand	111-116	6	19
α-helix	121-123	3
β-strand	125-133	9	18
α-helix	139	1
β-strand	140-142	3	18
β-strand	147-150	4	18

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ipilimumab-VH	A, D, G, J	protein	118	Homo sapiens
ipilimumab-VL	B, E, H, K	protein	109	Homo sapiens
Cytotoxic T-lymphocyte protein 4	C, F, I, L	protein	127	Homo sapiens	P16410 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>5XJ3_1 ipilimumab-VH (chains A, D, G, J)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYTMHWVRQAPGKGLEWVTFISYDGNNKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARTGWLGPFDYWGQGTLVTVSS

Sequence of entity 2 (B, E, H, K), FASTA

>5XJ3_2 ipilimumab-VL (chains B, E, H, K)
EIVLTQSPGTLSLSPGERATLSCRASQSVGSSYLAWYQQKPGQAPRLLIYGAFSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKR

Sequence of entity 3 (C, F, I, L), FASTA

>5XJ3_3 Cytotoxic T-lymphocyte protein 4 (chains C, F, I, L)
MKAMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNE
LTFLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDP
EPCPDSD

Primary citation

Remarkably similar CTLA-4 binding properties of therapeutic ipilimumab and tremelimumab antibodies. He, M., Chai, Y., Qi, J. et al. Oncotarget (2017) 8:67129-67139. DOI 10.18632/oncotarget.18004 · 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

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