8TBB: F9S, novel TIM-3 targeting antibody

F9S, novel TIM-3 targeting antibody, bound to IgV domain of TIM-3. Determined by X-ray diffraction at 2.5 Å resolution. Released 28 Aug 2024.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,315
Mol. weight: 60.06 kDa
Ligands: NAG
Released: 28 Aug 2024

Explore 8TBB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TBB contains 19 α-helices and 59 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 D: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
α-helix	12	1
β-strand	13-15	3	2
β-strand	18	1	3
β-strand	23	1	4
β-strand	26	1	4
β-strand	30-35	6	1
β-strand	45-49	5	1
β-strand	54-56	3	1
β-strand	61-63	3	2
β-strand	71	1	3
β-strand	74-76	3	2
α-helix	81-83	3
β-strand	85-91	7	1
β-strand	95-96	2	5
β-strand	100-108	9	1

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	5
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	5
β-strand	46-51	6	5
β-strand	57-60	4	5
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-98	7	5
β-strand	112-113	2	5
β-strand	114	1	6
β-strand	117-121	5	5
α-helix	125-126	2
β-strand	127	1	7
α-helix	128-129	2
β-strand	130-134	5	8
β-strand	145-155	11	8
β-strand	156	1	7
β-strand	161-164	4	9
α-helix	165-167	3
β-strand	169	1	9
β-strand	173-175	3	8
α-helix	176-178	3
β-strand	179-180	2	8
β-strand	186-195	10	8
α-helix	196-199	4
β-strand	204-210	7	9
α-helix	211-213	3
β-strand	215-221	7	9

Chain L: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-14	5	5
β-strand	19-25	7	10
β-strand	33-38	6	5
β-strand	45-49	5	5
β-strand	53-54	2	5
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	84-90	7	5
α-helix	96	1
β-strand	97-98	2	5
β-strand	99	1	10
β-strand	102-107	6	5
β-strand	111	1	11
α-helix	112-113	2
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	12
β-strand	140	1	11
β-strand	145-150	6	13
β-strand	153-154	2	13
α-helix	155	1
β-strand	159-163	5	12
β-strand	173-182	10	12
α-helix	183-188	6
β-strand	191-197	7	13
β-strand	205-210	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell immunoglobulin mucin receptor 3	D	protein	110	Homo sapiens	Q8TDQ0 (AlphaFold model)
F9S Fab heavy chain	H	protein	226	Homo sapiens
F9S Fab light chain	L	protein	214	Homo sapiens

Sequence of entity 1 (D), FASTA

>8TBB_1 T-cell immunoglobulin mucin receptor 3 (chains D)
SEVEYRAEVGQNAYLPCFYTPAAPGNLVPVCWGKGACPVFECGNVVLRTDERDVNYWTSR
YWLNGDFRKGDVSLTIENVTLADSGIYCCRIQIPGIMNDEKFNLKLVIKP

Sequence of entity 2 (H), FASTA

>8TBB_2 F9S Fab heavy chain (chains H)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYHMSWVRQAPGKGLEWVSAISGSGRSYYY
KDSFFGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCATSWETARILPGAFDIWGRGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 3 (L), FASTA

>8TBB_3 F9S Fab light chain (chains L)
DIQLTQSPSFLSASVGDRVTITCRTSQDTNSYLAWYQQKPGKAPKLLIYAASVLLSGVPS
RFSGSGSGTEFTLTISSLQPEDFATYYCQQLASSPITFGQGTRLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Generation of AZD7789, a novel PD-1 and TIM-3 targeting bispecific antibody, which binds to a differentiated epitope of TIM-3. Clancy-Thompson, E., Perry, T., Pryts, S. et al. To be published.

Other PDB entries of the same protein (UniProt Q8TDQ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M3Z 1.4 Å, Structure of TIM-3 in complex with N-(4-(8-chloro-2-mehtyl-5-oxo-5,6-dihydro-[1,2,4]triaz…
7KQL 1.49 Å, Anti-Tim3 antibody Fab complex
7M3Y 1.69 Å, Structure of TIM-3 in complex with 8-chloro-2-methyl-9-(3-mehtylpyridin-4-yl)-[1,2,4]tria…
6DHB 1.7 Å, Crystal structure of the human TIM-3 with bound Calcium
7M41 1.79 Å, Structure of TIM-3 in complex with N-(4-(8-chloro-2-methyl-5-oxo-5,6-dihydro-[1,2,4]traiz…
8TFT 2.3 Å, Fab of O13-1 human IgG1 antibody bound to IgV domain of human TIM-3
5F71 2.4 Å, Human T-cell immunoglobulin and mucin domain protein 3 (hTIM-3)
6TXZ 3.06 Å, FAB part of M6903 in complex with human TIM3
5DZL 3.4 Å, Crystal structure of the protein human CEACAM1
8HGJ 4.82 Å, Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3)…

Browse structure collections

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