8TFT: Fab of O13-1 human IgG1 antibody

Fab of O13-1 human IgG1 antibody bound to IgV domain of human TIM-3. Determined by X-ray diffraction at 2.3 Å resolution. Released 28 Aug 2024.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,313
Mol. weight: 118.77 kDa
Ligands: NAG
Released: 28 Aug 2024

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

Secondary structure: helices and β-sheets

8TFT contains 40 α-helices and 116 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 F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
α-helix	12	1
β-strand	13-15	3	3
β-strand	18	1	14
β-strand	30-34	5	13
β-strand	44-49	6	13
β-strand	54-56	3	13
β-strand	61-63	3	3
α-helix	67-69	3
β-strand	71	1	14
β-strand	74-76	3	3
α-helix	81-83	3
β-strand	85-91	7	13
β-strand	100-108	9	13

Chain G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	29
α-helix	12	1
β-strand	13-15	3	18
β-strand	18	1	30
β-strand	30-34	5	29
β-strand	45-49	5	29
β-strand	54-56	3	29
β-strand	61-63	3	18
α-helix	67-69	3
β-strand	71	1	30
β-strand	74-76	3	18
α-helix	81-83	3
β-strand	85-91	7	29
β-strand	100-108	9	29

Chain H: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11-12	2	16
β-strand	18-25	8	15
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	46-51	6	17
β-strand	58-60	3	17
α-helix	62-64	3
β-strand	68-73	6	15
α-helix	74-76	3
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-98	7	17
β-strand	103	1	18
β-strand	111-112	2	17
β-strand	116-118	3	17
β-strand	119-120	2	16
β-strand	126	1	19
α-helix	127-128	2
β-strand	129-133	5	20
β-strand	142	1	21
β-strand	144	1	21
β-strand	145-154	10	20
β-strand	155	1	19
β-strand	160-163	4	22
β-strand	172-174	3	20
α-helix	175-177	3
β-strand	178-179	2	20
β-strand	185-193	9	20
α-helix	195-197	3
β-strand	203-209	7	22
α-helix	210-212	3
β-strand	214-220	7	22

Chain I: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	58-60	3	2
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	2
β-strand	103	1	3
β-strand	111-112	2	2
β-strand	116-120	5	2
β-strand	126	1	4
α-helix	127-128	2
β-strand	129-133	5	5
β-strand	140	1	5
β-strand	144-154	11	5
β-strand	155	1	4
β-strand	160-163	4	6
β-strand	172-174	3	5
α-helix	175-177	3
β-strand	178-179	2	5
β-strand	185-194	10	5
α-helix	195-197	3
β-strand	203-209	7	6
α-helix	210-212	3
β-strand	214-220	7	6

Chains L and M: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	23
β-strand	9-12	4	24
β-strand	18-23	6	23
α-helix	27-29	3
β-strand	33-37	5	24
α-helix	42-43	2
β-strand	44-47	4	24
β-strand	48	1	25
β-strand	52	1	25
β-strand	61-66	6	23
β-strand	69-74	6	23
α-helix	79-81	3
β-strand	83-91	9	24
β-strand	96-99	4	24
β-strand	103-107	5	24
α-helix	110-112	3
β-strand	113	1	26
α-helix	114-115	2
β-strand	116-120	5	27
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	27
β-strand	142	1	26
β-strand	147-152	6	28
β-strand	155-157	3	28
β-strand	161-163	3	27
α-helix	164-166	3
β-strand	167-168	2	27
β-strand	174-182	9	27
α-helix	184-189	6
β-strand	193-199	7	28
β-strand	202-208	7	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O-13-1 IgG1 Fab heavy chain	H, I	protein	227	Homo sapiens
O-13-1 IgG1 Fab light chain	L, M	protein	213	Homo sapiens
T-cell immunoglobulin mucin receptor 3	F, G	protein	109	Homo sapiens	Q8TDQ0 (AlphaFold model)

Sequence of entity 1 (H, I), FASTA

>8TFT_1 O-13-1 IgG1 Fab heavy chain (chains H, I)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGSYGTYYGNYFEYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 2 (L, M), FASTA

>8TFT_2 O-13-1 IgG1 Fab light chain (chains L, M)
SYVLTQPPSVSVAPGKTARITCGGDNIGGKSVHWYQQKPGQAPVLVIYYDSDRPSGIPER
FSGSNSGNTATLTISRVEAGDEADYYCQVLDRRSDHWLFGGGTKLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

Sequence of entity 3 (F, G), FASTA

>8TFT_3 T-cell immunoglobulin mucin receptor 3 (chains F, G)
SEVEYRAEVGQNAYLPCFYTPAAPGNLVPVCWGKGACPVFECGNVVLRTDERDVNYWTSR
YWLNGDFRKGDVSLTIENVTLADSGIYCCRIQIPGIMNDEKFNLKLVIK

Ligands and cofactors

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

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…
5F71 2.4 Å, Human T-cell immunoglobulin and mucin domain protein 3 (hTIM-3)
8TBB 2.5 Å, F9S, novel TIM-3 targeting antibody, bound to IgV domain of TIM-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)…

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