7C88: Complex structure of JS003 and PD-L1

Complex structure of JS003 and PD-L1. Determined by X-ray diffraction at 2.0 Å resolution. Released 14 Apr 2021.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 8,992
Mol. weight: 127.35 kDa
Released: 14 Apr 2021

Explore 7C88 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7C88 contains 48 α-helices and 106 β-strands across 6 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: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	13
β-strand	30-31	2	14
β-strand	37-44	8	13
α-helix	45-49	5
β-strand	52-58	7	15
β-strand	64-71	8	15
β-strand	76-78	3	15
α-helix	83-85	3
β-strand	86-91	6	13
α-helix	92-94	3
β-strand	96-101	6	13
α-helix	106-108	3
β-strand	110-117	8	15
β-strand	126-127	2	15
β-strand	131-133	3	15
β-strand	134-135	2	14
α-helix	139-140	2
β-strand	141	1	16
α-helix	142-143	2
β-strand	144-148	5	17
β-strand	159-169	11	17
β-strand	170	1	16
β-strand	175-178	4	18
α-helix	179-181	3
β-strand	187-189	3	17
α-helix	190-192	3
β-strand	193-194	2	17
β-strand	200-209	10	17
α-helix	210-212	3
β-strand	219-224	6	18
α-helix	225-227	3
β-strand	229-234	6	18

Chains B and L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	19
β-strand	32-36	5	20
β-strand	41-47	7	19
β-strand	55-60	6	20
β-strand	67-71	5	20
β-strand	75-76	2	20
α-helix	77	1
β-strand	84-89	6	19
β-strand	92-97	6	19
α-helix	102-104	3
β-strand	106-112	7	20
α-helix	118	1
β-strand	119-120	2	20
β-strand	124-129	6	20
β-strand	133	1	21
α-helix	134-135	2
β-strand	136-140	5	22
α-helix	141-143	3
α-helix	144-148	5
β-strand	151-161	11	22
β-strand	162	1	21
β-strand	167-172	6	23
β-strand	175-176	2	23
α-helix	177	1
β-strand	181-185	5	22
α-helix	186-189	4
β-strand	195-204	10	22
α-helix	205-209	5
β-strand	213-219	7	23
β-strand	227-232	6	23

Chain C: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	24
β-strand	27-30	4	25
β-strand	36-41	6	24
α-helix	50-52	3
β-strand	54-59	6	25
β-strand	62-68	7	25
β-strand	71-72	2	25
α-helix	74-76	3
α-helix	79-81	3
β-strand	85-87	3	24
α-helix	89-91	3
β-strand	96-101	6	24
α-helix	106-108	3
β-strand	110-118	9	25
β-strand	120-130	11	25
α-helix	131-133	3

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	1
β-strand	30-31	2	2
β-strand	37-44	8	1
α-helix	45-49	5
β-strand	52-58	7	3
β-strand	64-71	8	3
β-strand	76-78	3	3
β-strand	86-91	6	1
β-strand	96-101	6	1
α-helix	106-108	3
β-strand	110-117	8	3
β-strand	126-127	2	3
β-strand	131-133	3	3
β-strand	134-135	2	2
α-helix	139-140	2
β-strand	141	1	4
α-helix	142-143	2
β-strand	144-148	5	5
β-strand	159-169	11	5
β-strand	170	1	4
β-strand	175-178	4	6
α-helix	179-181	3
β-strand	187-189	3	5
α-helix	190-192	3
β-strand	193-194	2	5
β-strand	200-209	10	5
α-helix	210-212	3
β-strand	219-224	6	6
α-helix	225-227	3
β-strand	229-234	6	6

Chain M: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	11
β-strand	27-30	4	12
β-strand	36-41	6	11
α-helix	50-52	3
β-strand	54-59	6	12
β-strand	62-68	7	12
β-strand	71-72	2	12
α-helix	74-76	3
α-helix	79-81	3
β-strand	85-87	3	11
α-helix	90-94	5
β-strand	96-101	6	11
α-helix	106-108	3
β-strand	110-118	9	12
β-strand	120-130	11	12
α-helix	131-133	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
JS003 Heavy chain	A, H	protein	228	Mus musculus
JS003 Light chain	B, L	protein	214	Mus musculus
Programmed cell death 1 ligand 1	C, M	protein	136	Homo sapiens	Q9NZQ7 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>7C88_1 JS003 Heavy chain (chains A, H)
QGQLQESGPSLVKPSQTLSLTCTVSGDSITRGYWNWIRKHPGKGLEYIGYISYTGSTYSN
LSLKSRVTISRDTSKNQYYLKLSSVTAADTAVYYCATSTGWLDPVDYWGQGTLVTVSSAS
TKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPPCPPCP

Sequence of entity 2 (B, L), FASTA

>7C88_2 JS003 Light chain (chains B, L)
DIVMTQSPDSLAVSLGERATINCKASQNVDTSVAWFQQKPGQPPKALIYSASFRYSGVPD
RFSGSGSGTDFTLTISSLQAEDVAVYFCQQYYGYPFTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, M), FASTA

>7C88_3 Programmed cell death 1 ligand 1 (chains C, M)
MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEME
DKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGG
ADYKRITVKVNAPYNK

Primary citation

Identification of a hotspot on PD-L1 for pH-dependent binding by monoclonal antibodies for tumor therapy. Liu, H., Bi, X., Zhou, Y. et al. Signal Transduct Target Ther (2020) 5:158-158. DOI 10.1038/s41392-020-00254-z · PubMed

Other PDB entries of the same protein (UniProt Q9NZQ7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5O45 0.99 Å, Structure of human PD-L1 in complex with inhibitor
8ALX 1.1 Å, Structure of human PD-L1 in complex with inhibitor
6NP9 1.27 Å, PD-L1 IgV domain V76T with fragment
9I0U 1.46 Å, Structure of human PD-L1 in complex with clinically evaluated inhibitor
6YCR 1.54 Å, Structure of human PD-L1 in complex with inhibitor
8AOK 1.6 Å, Complex of PD-L1 with VHH6
13DT 1.64 Å, Structure of FabS1CE2_P4a in complex with the N-terminal domain of PD-L1
7CZD 1.64 Å, Crystal structure of PD-L1 in complex with a VHH
5JDS 1.7 Å, Crystal structure of PD-L1 complexed with a nanobody at 1.7 Angstron resolution
5N2F 1.7 Å, Structure of PD-L1/small-molecule inhibitor complex
9QSM 1.75 Å, small molecule inhibitor in complex with PD-L1
8ZNL 1.77 Å, PD-L1 de novo designed binder with picomolar binding affinity

Browse structure collections

About this viewer

MolViewer shows 7C88 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.