7E9B: Heavy chain of Fab fragment of HLX10

Structural basis of HLX10 PD-1 receptor recognition, a promising anti-PD-1 antibody clinical candidate for cancer immunotherapy. Determined by X-ray diffraction at 1.78 Å resolution. Released 28 Jul 2021.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,600
Mol. weight: 59.21 kDa
Released: 28 Jul 2021

Explore 7E9B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E9B contains 19 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: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
β-strand	36-38	3	13
β-strand	41-45	5	14
β-strand	50-55	6	13
β-strand	63-70	8	14
β-strand	76-82	7	14
β-strand	95-99	5	13
β-strand	105-110	6	13
α-helix	115-117	3
β-strand	119-127	9	14
β-strand	131	1	9
β-strand	133-136	4	14
α-helix	137-139	3
β-strand	140-145	6	14

Chain H: 7 helices, 22 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	92-100	9	3
β-strand	102-106	5	3
β-strand	110-112	3	3
β-strand	113-114	2	2
β-strand	120	1	4
α-helix	121-122	2
β-strand	123-127	5	5
β-strand	138-148	11	5
β-strand	149	1	4
β-strand	154-157	4	6
α-helix	158-160	3
β-strand	166-168	3	5
α-helix	169-171	3
β-strand	172-173	2	5
β-strand	179-188	10	5
α-helix	189-193	5
β-strand	198-203	6	6
α-helix	204-206	3
β-strand	208-213	6	6

Chain L: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
β-strand	93	1	9
α-helix	96	1
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	145-150	6	12
β-strand	153-154	2	12
α-helix	155	1
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-187	5
β-strand	191-197	7	12
β-strand	205-210	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
heavy chain of Fab fragment of HLX10	H	protein	215	Homo sapiens
light chain of Fab fragment of HLX10	L	protein	214	Homo sapiens
Programmed cell death protein 1	C	protein	115	Homo sapiens	Q15116 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7E9B_1 heavy chain of Fab fragment of HLX10 (chains H)
QVQLVESGGGLVKPGGSLRLSCAASGFTFSNYGMSWIRQAPGKGLEWVSTISGGGSNIYY
ADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCVSYYYGIDFWGQGTSVTVSSASTK
GPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE

Sequence of entity 2 (L), FASTA

>7E9B_2 light chain of Fab fragment of HLX10 (chains L)
DIQMTQSPSSLSASVGDRVTITCKASQDVTTAVAWYQQKPGKAPKLLIYWASTRHTGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQHYTIPWTFGGGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>7E9B_3 Programmed cell death protein 1 (chains C)
WNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQ
DCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTE

Primary citation

Structural basis of HLX10 PD-1 receptor recognition, a promising anti-PD-1 antibody clinical candidate for cancer immunotherapy. Issafras, H., Fan, S., Tseng, C.L. et al. PLoS One (2021) 16:e0257972-e0257972. DOI 10.1371/journal.pone.0257972 · PubMed

Other PDB entries of the same protein (UniProt Q15116 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UMU 1.18 Å, Human apo PD-1 triple mutant
6J14 1.4 Å, Complex structure of GY-14 and PD-1
6UMV 1.42 Å, Human apo PD-1 double mutant
7WSL 1.53 Å, PD-1 in complex with Dostarlimab
9EHT 1.54 Å, Crystal Structure of PD-1/retifanlimab complex
7VUX 1.64 Å, Complex structure of PD1 and 609A-Fab
8EQ6 1.65 Å, PD1 signaling receptor bound to FAB Complex
6K0Y 1.7 Å, Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor
9Q8L 1.85 Å, Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution
8GY5 1.98 Å, High-resolution structure of the cemiplimab Fab in complex with PD-1
6UMT 1.99 Å, High-affinity human PD-1 PD-L2 complex
5GGS 2.0 Å, PD-1 in complex with pembrolizumab Fab

Browse structure collections

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