13DT: FabS1CE2_P4a

Structure of FabS1CE2_P4a in complex with the N-terminal domain of PD-L1. Determined by X-ray diffraction at 1.64 Å resolution. Released 30 Sept 2026.

Method: X-ray diffraction
Resolution: 1.64 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,992
Mol. weight: 64.79 kDa
Ligands: CIT, NAG
Released: 30 Sept 2026

Explore 13DT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

13DT contains 25 α-helices and 57 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: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	17-25	9	1
α-helix	29-31	3
β-strand	33-39	7	3
β-strand	46-52	7	3
β-strand	57-60	4	3
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	109-110	2	3
β-strand	114-116	3	3
β-strand	117-118	2	2
β-strand	123	1	4
α-helix	124-125	2
β-strand	126-130	5	5
α-helix	131-133	3
β-strand	138	1	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	201-206	6	6
α-helix	207-209	3
β-strand	211-216	6	6

Chain B: 9 helices, 21 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
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-198	8	11
β-strand	201-208	8	11

Chain C: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	12
β-strand	27-31	5	13
β-strand	36-38	3	14
β-strand	41	1	12
α-helix	48	1
α-helix	50-52	3
β-strand	54-59	6	13
β-strand	62-68	7	13
β-strand	71-72	2	13
α-helix	74-76	3
α-helix	79-81	3
β-strand	85-87	3	14
α-helix	89-94	6
β-strand	96	1	12
β-strand	99-101	3	14
α-helix	106-108	3
β-strand	110-117	8	13
β-strand	121-131	11	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
FabS1CE2_P4a heavy chain	A	protein	227	Homo sapiens
FabS1CE2_P4a light chain (Trastuzumab Fab Light Chain)	B	protein	217	Homo sapiens
Programmed cell death 1 ligand 1	C	protein	126	Homo sapiens	Q9NZQ7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>13DT_1 FabS1CE2_P4a heavy chain (chains A)
EVQLVESGGGLVQPGGSLRLSCAASGFTLENYDIHWVRQAPGKGLEWVAWIYPRNGFTAY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARLLWYDIHAMDYWGQGTLVTVFN
QIQGPSVFPLAPSSKSTSGGTAALGCLVKDYFPGPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (B), FASTA

>13DT_2 FabS1CE2_P4a light chain (Trastuzumab Fab Light Chain) (chains B)
AAAVADIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLY
SGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVSWYVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>13DT_3 Programmed cell death 1 ligand 1 (chains C)
FTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQH
SSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNALVPRGS
HHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (NA, PEG, EDO) are not listed.

Primary citation

Strategy for modular assembly of tetravalent, multispecific antibodies. Mallette, E., Blazer, L.L., Hokanson, C.A. et al. Protein Sci (2026) 35:e70797-e70797. DOI 10.1002/pro.70797 · 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
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
5C3T 1.8 Å, PD-1 binding domain from human PD-L1

Browse structure collections

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