7SU1: Acidic pH-selective Ipilimumab variant Ipi.106

Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.106 in complex with CTLA-4. Determined by X-ray diffraction at 2.53 Å resolution. Released 2 Mar 2022.

Method: X-ray diffraction
Resolution: 2.53 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,155
Mol. weight: 62.09 kDa
Ligands: NAG
Released: 2 Mar 2022

Explore 7SU1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SU1 contains 16 α-helices and 55 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	13
β-strand	10-12	3	9
β-strand	18-26	9	13
β-strand	33-41	9	9
β-strand	46-55	10	9
β-strand	60	1	13
β-strand	68-73	6	13
β-strand	76-82	7	13
α-helix	86-88	3
β-strand	91-100	10	9
α-helix	104	1
β-strand	105-108	4	9
β-strand	112-115	4	9

Chain H: 7 helices, 23 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	46-51	6	3
β-strand	57-59	3	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	3
β-strand	100A-103	4	3
β-strand	107-109	3	3
β-strand	110-111	2	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-185	10	5
α-helix	186-190	5
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-28	11	7
α-helix	30-32	3
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
β-strand	62-75	14	7
α-helix	80-82	3
β-strand	85-90	6	8
β-strand	93	1	9
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	144-150	7	12
β-strand	154	1	12
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-188	6
β-strand	191-198	8	12
β-strand	205-210	6	12

Molecules and chains

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

Sequence of entity 1 (H), FASTA

>7SU1_1 Fab heavy chain (chains H)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSHYTMHWVRQAPGKGLEWVTFISYDGHNKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARHGWLGPFDYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCGGHHHHHH

Sequence of entity 2 (L), FASTA

>7SU1_2 Fab light chain (chains L)
EIVLTQSPGTLSLSPGERATLSCRASQEVGESELAWYQQKPGQAPRLLIYGAFSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>7SU1_3 Cytotoxic T-lymphocyte protein 4 (chains C)
KAMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNEL
TFLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDGH
HHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Improved therapeutic index of an acidic pH-selective antibody. Lee, P.S., MacDonald, K.G., Massi, E. et al. MAbs (2022) 14:2024642-2024642. DOI 10.1080/19420862.2021.2024642 · 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…
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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