6HIG: HPD-1/NBO1a Fab complex

hPD-1/NBO1a Fab complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 5 Jun 2019.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,942
Mol. weight: 61.73 kDa
Released: 5 Jun 2019

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

Secondary structure: helices and β-sheets

6HIG contains 17 α-helices and 56 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 B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	11
β-strand	41-45	5	12
β-strand	46	1	13
β-strand	48	1	13
β-strand	50-55	6	11
β-strand	65-68	4	14
β-strand	78-82	5	14
β-strand	95-99	5	11
β-strand	105-110	6	11
α-helix	115-117	3
β-strand	119-121	3	12
β-strand	122-125	4	14
β-strand	135-136	2	14
α-helix	138-139	2
β-strand	140-145	6	12

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	104-107	4	2
β-strand	111-115	5	2
β-strand	121	1	3
β-strand	124-128	5	4
β-strand	139-149	11	4
β-strand	150	1	3
β-strand	155-158	4	5
α-helix	159-161	3
β-strand	163	1	5
β-strand	167-169	3	4
α-helix	170-172	3
β-strand	173-174	2	4
β-strand	180-189	10	4
α-helix	190-192	3
β-strand	199-204	6	5
α-helix	205-207	3
β-strand	209-214	6	5

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-154	2	10
α-helix	155	1
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-197	7	10
β-strand	205-210	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy Chain	H	protein	233	Mus musculus
Light Chain	L	protein	214	Mus musculus
Programmed cell death protein 1	B	protein	118	Homo sapiens	Q15116 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6HIG_1 Heavy Chain (chains H)
EVQLVQSGAEVKKPGESLKISCKGSGYSFTNFYIHWVRQAPGQRLEWMGSIYPNYGDTAY
NQKFKDRFVFSLDTSVSTAYLQISSLKAEDTAVYYCARGYSYAMDYWGQGTTVTVSSAST
KGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPPCPSCPAPEFLG

Sequence of entity 2 (L), FASTA

>6HIG_2 Light Chain (chains L)
DIQMTQSPSSVSASVGDRVTITCSASQGISGDLNWYQQKPGKAPKLLIYHTSSLHSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQYYSKDLLTFGGGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (B), FASTA

>6HIG_3 Programmed cell death protein 1 (chains B)
NPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQD
SRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAE

Primary citation

Tumor suppression of novel anti-PD-1 antibodies mediated through CD28 costimulatory pathway. Fenwick, C., Loredo-Varela, J.L., Joo, V. et al. J Exp Med (2019) 216:1525-1541. DOI 10.1084/jem.20182359 · 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
7E9B 1.78 Å, Structural basis of HLX10 PD-1 receptor recognition, a promising anti-PD-1 antibody…
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

Browse structure collections

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