6RQM: A blocking anti-CTLA-4 Nanobody

A blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4. Determined by X-ray diffraction at 3.0 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Camelus bactrianus, Homo sapiens
Chains: 2
Atoms: 1,781
Mol. weight: 28.69 kDa
Released: 8 Jul 2020

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

Secondary structure: helices and β-sheets

6RQM contains 4 α-helices and 23 β-strands across 2 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	4
β-strand	20-26	7	4
β-strand	33-41	9	5
β-strand	46-55	10	5
β-strand	60-63	4	5
β-strand	68-72	5	4
β-strand	76-81	6	4
α-helix	86-88	3
β-strand	90-100	11	5
α-helix	104	1
β-strand	105-108	4	5
α-helix	109-111	3
β-strand	112-114	3	5

Chain B: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	11-12	2	2
β-strand	17-24	8	1
β-strand	33-39	7	3
β-strand	45-52	8	3
β-strand	58-60	3	3
β-strand	65	1	1
β-strand	68-73	6	1
β-strand	78-84	7	1
β-strand	92-99	8	3
α-helix	103-106	4
β-strand	117-118	2	3
β-strand	122-124	3	3
β-strand	125-126	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
A blocking anti-CTLA-4 nanobody (KN044)	B	protein	144	Camelus bactrianus
Cytotoxic T-lymphocyte protein 4	A	protein	125	Homo sapiens	P16410 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>6RQM_1 A blocking anti-CTLA-4 nanobody (KN044) (chains B)
QVQLVESGGGLVQPGGSLRLSCAASGYIYSAYCMGWFRQAPGKGLEGVAAIYIGGGSTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAADVIPTETCLGGSWSGPFGYWGQ
GTLVTVSSGSMDPGGSHHHHHHHH

Sequence of entity 2 (A), FASTA

>6RQM_2 Cytotoxic T-lymphocyte protein 4 (chains A)
AMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNELT
FLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDPEP
CPDSD

Primary citation

A blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4. Gao, H., 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
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

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