7KQL: Anti-Tim3 antibody Fab complex

Anti-Tim3 antibody Fab complex. Determined by X-ray diffraction at 1.49 Å resolution. Released 9 Feb 2022.

Method: X-ray diffraction
Resolution: 1.49 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,890
Mol. weight: 63.24 kDa
Released: 9 Feb 2022

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

Secondary structure: helices and β-sheets

7KQL contains 24 α-helices and 53 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 H: 9 helices, 22 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	35-41	7	3
β-strand	48-54	7	3
β-strand	59-61	3	3
α-helix	63-68	6
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-100	8	3
β-strand	113	1	3
β-strand	117-119	3	3
β-strand	120-121	2	2
α-helix	125-126	2
β-strand	127	1	4
α-helix	128-129	2
β-strand	130-134	5	5
β-strand	146-155	10	5
β-strand	156	1	4
β-strand	161-164	4	6
α-helix	165-167	3
β-strand	173-175	3	5
α-helix	176-178	3
β-strand	179-180	2	5
β-strand	186-194	9	5
α-helix	196-198	3
β-strand	205-210	6	6
α-helix	211-213	3
β-strand	215-220	6	6
α-helix	223-225	3

Chain L: 11 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
α-helix	28-29	2
α-helix	30-32	3
β-strand	34-39	6	8
β-strand	46-50	5	8
β-strand	54-55	2	8
α-helix	56	1
β-strand	63-68	6	7
β-strand	71-76	6	7
α-helix	81-83	3
β-strand	85-91	7	8
α-helix	97	1
β-strand	98-99	2	8
β-strand	103-107	5	8
β-strand	112	1	9
α-helix	113-114	2
β-strand	115-119	5	10
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	10
β-strand	141	1	9
β-strand	146-151	6	11
β-strand	154-155	2	11
α-helix	156	1
β-strand	160-164	5	10
α-helix	165-168	4
β-strand	174-183	10	10
α-helix	184-188	5
β-strand	192-198	7	11
β-strand	206-211	6	11

Chain T: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	12
β-strand	13-15	3	13
β-strand	18	1	14
β-strand	30-34	5	12
β-strand	45-47	3	12
α-helix	56-58	3
β-strand	61-63	3	13
α-helix	67-69	3
β-strand	71	1	14
α-helix	73	1
β-strand	74-76	3	13
α-helix	81-83	3
β-strand	85-91	7	12
β-strand	100-109	10	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tim3.18 Fab heavy chain	H	protein	234	Homo sapiens
Tim3.18 Fab light chain	L	protein	215	Homo sapiens
Hepatitis A virus cellular receptor 2	T	protein	129	Homo sapiens	Q8TDQ0 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7KQL_1 Tim3.18 Fab heavy chain (chains H)
QLQLQESGPGLVKPSETLSLTCTVSGGSISSRSYYWGWIRQPPGKGLEWIGSIYYSGFTY
YQPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCATGGPYGDYAHWFEPWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCGGHHHHHH

Sequence of entity 2 (L), FASTA

>7KQL_2 Tim3.18 Fab light chain (chains L)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPITFGQGTRLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (T), FASTA

>7KQL_3 Hepatitis A virus cellular receptor 2 (chains T)
HHHHHHSAALEVLFQGPGSEVEYRAEVGQNAYLPCFYTPAAPGNLVPVCWGKGACPVFEC
GNVVLRTDERDVNYWTSRYWLNGDFRKGDVSLTIENVTLADSGIYCCRIQIPGIMNDEKF
NLKLVIKPA

Primary citation

Tim-3 mediates T cell trogocytosis to limit antitumor immunity. Pagliano, O., Morrison, R.M., Chauvin, J.M. et al. J Clin Invest (2022) 132. DOI 10.1172/JCI152864 · PubMed

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…
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)
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)…

Browse structure collections

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