9DQ3: Engineered Ipilimumab (mipi.4) Fab

Crystal structure of engineered Ipilimumab (mipi.4) Fab in complex with human CTLA-4. Determined by X-ray diffraction at 1.64 Å resolution. Released 5 Feb 2025.

Method: X-ray diffraction
Resolution: 1.64 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,274
Mol. weight: 61.87 kDa
Released: 5 Feb 2025

Explore 9DQ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DQ3 contains 17 α-helices and 53 β-strands across 3 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	10-12	3	2
β-strand	19-25	7	1
β-strand	33-42	10	2
β-strand	45-55	11	2
β-strand	68-72	5	1
β-strand	76-81	6	1
β-strand	91-100	10	2
α-helix	104	1
β-strand	105-108	4	2
β-strand	112-115	4	2

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	10-12	3	4
β-strand	18-25	8	3
α-helix	29-31	3
β-strand	34-39	6	4
β-strand	46-51	6	4
β-strand	58-60	3	4
β-strand	68-73	6	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-99	8	4
α-helix	100	1
β-strand	105-108	4	4
β-strand	112-116	5	4
β-strand	122	1	5
α-helix	123-124	2
β-strand	125-129	5	6
β-strand	140-150	11	6
β-strand	151	1	5
β-strand	156-159	4	7
α-helix	160-162	3
β-strand	168-170	3	6
α-helix	171-173	3
β-strand	174-175	2	6
β-strand	181-190	10	6
α-helix	191-195	5
β-strand	199-205	7	7
α-helix	206-208	3
β-strand	210-216	7	7

Chain L: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-13	4	9
β-strand	19-25	7	8
β-strand	34-39	6	9
β-strand	46-50	5	9
β-strand	54-55	2	9
α-helix	56	1
β-strand	63-68	6	8
β-strand	71-76	6	8
α-helix	81-83	3
β-strand	86-91	6	9
β-strand	94	1	2
α-helix	97	1
β-strand	98-99	2	9
β-strand	103-107	5	9
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	145-151	7	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	184-188	5
β-strand	192-199	8	12
β-strand	206-211	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytotoxic T-lymphocyte protein 4	C	protein	125	Homo sapiens	P16410 (AlphaFold model)
mipi.4 heavy chain	H	protein	229	Homo sapiens
mipi.4 light chain	L	protein	215	Homo sapiens

Sequence of entity 1 (C), FASTA

>9DQ3_1 Cytotoxic T-lymphocyte protein 4 (chains C)
KAMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNEL
TFLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDGH
HHHHH

Sequence of entity 2 (H), FASTA

>9DQ3_2 mipi.4 heavy chain (chains H)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSKYVMHWVRQAPGKGLEWVTGISYDGRHKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARTGWLGPFDYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCGGHHHHHH

Sequence of entity 3 (L), FASTA

>9DQ3_3 mipi.4 light chain (chains L)
EIVLTQSPGTLSLSPGERATLSCRQSQSVGWSPLAWYQQKPGQAPRLLIYGAFSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Engineered ipilimumab variants that bind human and mouse CTLA-4. Robison, B., Diong, S.J., Kumar, A. et al. MAbs (2025) 17:2451296-2451296. DOI 10.1080/19420862.2025.2451296 · 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
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
1I8L 3.0 Å, Human B7-1/CTLA-4 co-stimulatory complex

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