6K0Y: Antibody Heavy Chain

Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor. Determined by X-ray diffraction at 1.7 Å resolution. Released 11 Dec 2019.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,684
Mol. weight: 62.93 kDa
Released: 11 Dec 2019

Explore 6K0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K0Y contains 24 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 A: 9 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
β-strand	35-40	6	3
β-strand	47-52	6	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	3
β-strand	108-109	2	3
β-strand	113-115	3	3
β-strand	116-117	2	2
α-helix	121-122	2
β-strand	123	1	4
α-helix	124-125	2
β-strand	126-130	5	5
β-strand	141-151	11	5
β-strand	152	1	4
β-strand	157-160	4	6
α-helix	161-163	3
β-strand	165	1	6
β-strand	169-171	3	5
α-helix	172-174	3
β-strand	175-176	2	5
β-strand	182-191	10	5
α-helix	192-194	3
β-strand	200-206	7	6
α-helix	207-209	3
β-strand	211-217	7	6

Chain B: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-14	5	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	62-65	4	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	102-107	6	8
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-125	4
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

Chain C: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	36-38	3	13
β-strand	41-45	5	14
β-strand	50-55	6	13
β-strand	63-70	8	14
α-helix	75	1
β-strand	76-82	7	14
α-helix	84-86	3
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
α-helix	146-147	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody Heavy Chain	A	protein	218	Homo sapiens
Antibody Light Chain	B	protein	214	Homo sapiens
Programmed cell death protein 1	C	protein	143	Homo sapiens	Q15116 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6K0Y_1 Antibody Heavy Chain (chains A)
QVQLQESGPGLVKPSETLSLTCAVSGHSIRGSYFWGWIRQPPGRGLEWIGSIYHSGSTYT
NPSLKSRATISVDTSKNQFSLKLNSVTAADTAVYYCARDLDIATTRDYWGQGTLVTVSSA
STKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE

Sequence of entity 2 (B), FASTA

>6K0Y_2 Antibody Light Chain (chains B)
DIQLTQSPSFLSASVGDRVTIICRASQGINNYLAWYQQKPGKAPKLLIYAASTLQSGVPS
RFSGSGSGTEFTLTISSLQPEDFATYYCQQLDSYPRTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>6K0Y_3 Programmed cell death protein 1 (chains C)
LDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPE
DRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRV
TERRAEVPTAHPSPSPRPAGQFQ

Primary citation

Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor. Liu, J., Wang, G., Liu, L. et al. Sci Rep (2019) 9:17830-17830. DOI 10.1038/s41598-019-54231-w · 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
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
5GGS 2.0 Å, PD-1 in complex with pembrolizumab Fab

Browse structure collections

About this viewer

MolViewer shows 6K0Y directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.