9LQI: Nanobody-161

Structure of Nanobody-161 in complex of Tumor necrosis factor receptor 2 (TNFR2). Determined by X-ray diffraction at 2.95 Å resolution. Released 5 Aug 2026.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Vicugna pacos, Homo sapiens
Chains: 4
Atoms: 4,339
Mol. weight: 76.28 kDa
Released: 5 Aug 2026

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

Secondary structure: helices and β-sheets

9LQI contains 14 α-helices and 66 β-strands across 4 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: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-12	3	25
β-strand	19-24	6	24
β-strand	30-39	10	25
β-strand	45-51	7	25
β-strand	58-60	3	25
β-strand	69-73	5	24
β-strand	78-82	5	24
α-helix	88-90	3
β-strand	92-101	10	25
β-strand	106	1	18
β-strand	108-111	4	25
β-strand	115-119	5	25

Chain B: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	30	1	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	69-73	5	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	101	1	3
β-strand	106	1	4
β-strand	108-111	4	2
β-strand	115-119	5	2

Chain C: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	14
β-strand	30-33	4	14
β-strand	35	1	15
β-strand	39-43	5	16
β-strand	52-55	4	16
β-strand	60-61	2	17
β-strand	66	1	15
α-helix	71	1
β-strand	72-73	2	17
α-helix	74-78	5
β-strand	82-86	5	18
β-strand	95-98	4	18
α-helix	99	1
β-strand	102-107	6	19
β-strand	112-117	6	19
α-helix	118-119	2
β-strand	121	1	20
β-strand	125-129	5	21
β-strand	138-141	4	21
α-helix	142-143	2
β-strand	146-147	2	22
β-strand	152	1	20
β-strand	158-159	2	22
α-helix	160-163	4
β-strand	166-168	3	23
β-strand	177-178	2	23

Chain R: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	5
β-strand	30-33	4	5
β-strand	35	1	6
β-strand	39-45	7	7
β-strand	50-55	6	7
β-strand	60-61	2	8
β-strand	66	1	6
α-helix	71	1
β-strand	72-73	2	8
α-helix	74-78	5
β-strand	82-86	5	4
β-strand	95-98	4	4
α-helix	99	1
β-strand	102-107	6	9
β-strand	112-117	6	9
α-helix	118-119	2
β-strand	121	1	10
β-strand	125-129	5	11
β-strand	138-141	4	11
α-helix	142-143	2
β-strand	146-147	2	12
β-strand	152	1	10
β-strand	158-159	2	12
α-helix	160-163	4
β-strand	166-168	3	13
β-strand	177-178	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nanobody-161 (B chain)	A, B	protein	121	Vicugna pacos
Tumor necrosis factor receptor superfamily member 1B	C, R	protein	235	Homo sapiens	P20333 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9LQI_1 Nanobody-161 (B chain) (chains A, B)
EVQLVESGGGLVQPGGSLRLSCAASGSIRFINDMGWYRQAPGKGLELVAAIGRGGGSTNY
ADSVKGRFTISRDNAKNTLYLQMNSLRAEDTAVYYCHAEISQLGYAFRDYWGQGTLVTVS
S

Sequence of entity 2 (C, R), FASTA

>9LQI_2 Tumor necrosis factor receptor superfamily member 1B (chains C, R)
LPAQVAFTPYAPEPGSTCRLREYYDQTAQMCCSKCSPGQHAKVFCTKTSDTVCDSCEDST
YTQLWNWVPECLSCGSRCSSDQVETQACTREQNRICTCRPGWYCALSKQEGCRLCAPLRK
CRPGFGVARPGTETSDVVCKPCAPGTFSNTTSSTDICRPHQICNVVAIPGNASMDAVCTS
TSPTRSMAPGAVHLPQPVSTRSQHTQPTPEPSTAPSTSFLLPMGPSPPAEGSTGD

Primary citation

Structure of Nanobody-161 in complex of Tumor necrosis factor receptor 2 (TNFR2) reveals a non-blocking mechanism for cancer therap. Fan, S., Lang, G., Zhou, J. To be published.

Other PDB entries of the same protein (UniProt P20333 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CU8 1.96 Å, Crystal Structure of TNFR2 TNFR2_mb1 Complex
1CA9 2.3 Å, Structure of tnf receptor associated factor 2 in complex with a peptide from tnf-R2
3ALQ 3.0 Å, Crystal structure of TNF-TNFR2 complex
8HLB 3.63 Å, Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2
9LFL 3.73 Å, Cryo-EM structure of linker-extended biparatopic antibody BA1-GP4 in complex with TNFR2

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