6TXZ: FAB part of M6903

FAB part of M6903 in complex with human TIM3. Determined by X-ray diffraction at 3.06 Å resolution. Released 8 Apr 2020.

Method: X-ray diffraction
Resolution: 3.06 Å
Organism: Homo sapiens
Chains: 12
Atoms: 16,053
Mol. weight: 236.81 kDa
Released: 8 Apr 2020

Explore 6TXZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TXZ contains 52 α-helices and 244 β-strands across 12 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: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	1
β-strand	34-36	3	2
β-strand	39	1	3
β-strand	51-55	5	1
β-strand	66-70	5	1
β-strand	75-77	3	1
β-strand	79	1	2
β-strand	82-84	3	2
α-helix	88-90	3
β-strand	92	1	3
β-strand	95-97	3	2
α-helix	102-104	3
β-strand	106-112	7	1
β-strand	116-117	2	4
β-strand	121-129	9	1

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	5
β-strand	34-36	3	6
β-strand	39	1	7
β-strand	51-55	5	5
β-strand	66-70	5	5
β-strand	75-78	4	5
β-strand	82-84	3	6
α-helix	88-90	3
β-strand	92	1	7
β-strand	95-97	3	6
α-helix	102-104	3
β-strand	106-112	7	5
β-strand	116-117	2	8
β-strand	121-129	9	5

Chains C and D: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	9
β-strand	34-36	3	10
β-strand	39	1	11
β-strand	51-55	5	9
β-strand	66-70	5	9
β-strand	75-78	4	9
β-strand	82-84	3	10
α-helix	88-90	3
β-strand	92	1	11
β-strand	95-97	3	10
α-helix	102-104	3
β-strand	106-112	7	9
β-strand	116-117	2	12
β-strand	121-129	9	9

Chain H: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11-12	2	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	4
β-strand	45-51	7	4
β-strand	57-60	4	4
β-strand	68-73	6	17
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-99	8	4
β-strand	104-107	4	4
β-strand	109	1	17
β-strand	111-113	3	4
β-strand	114-115	2	18
β-strand	121	1	19
α-helix	122-123	2
β-strand	124-131	8	20
β-strand	139-149	11	20
β-strand	150	1	19
β-strand	155-158	4	21
β-strand	163	1	21
β-strand	167-169	3	20
α-helix	170-172	3
β-strand	173-174	2	20
β-strand	180-189	10	20
β-strand	198-204	7	21
α-helix	205-207	3
β-strand	209-215	7	21

Chain I: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	11-12	2	23
β-strand	18-25	8	22
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	57-60	4	8
β-strand	68-73	6	22
β-strand	78-83	6	22
α-helix	88-90	3
β-strand	92-98	7	8
β-strand	99	1	24
β-strand	104	1	24
β-strand	111-113	3	8
β-strand	114-115	2	23
β-strand	121	1	25
α-helix	122-123	2
β-strand	124-128	5	26
β-strand	139-149	11	26
β-strand	150	1	25
β-strand	155-158	4	27
β-strand	163	1	27
β-strand	167-169	3	26
α-helix	170-172	3
β-strand	173-174	2	26
β-strand	180-189	10	26
β-strand	198-204	7	27
α-helix	205-207	3
β-strand	209-215	7	27

Chain J: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	28
β-strand	11-12	2	29
β-strand	18-25	8	28
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	57-60	4	12
β-strand	68-73	6	28
β-strand	78-83	6	28
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	104-107	4	12
β-strand	109	1	28
β-strand	111-113	3	12
β-strand	114-115	2	29
α-helix	119-120	2
β-strand	121	1	30
α-helix	122-123	2
β-strand	124-128	5	31
β-strand	141-149	9	31
β-strand	150	1	30
β-strand	155-158	4	32
β-strand	163	1	32
β-strand	167-169	3	31
α-helix	170-172	3
β-strand	173-174	2	31
β-strand	180-187	8	31
β-strand	193	1	33
β-strand	196	1	33
β-strand	199-204	6	32
α-helix	205-207	3
β-strand	209-214	6	32

Chain K: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	34
β-strand	11-12	2	35
β-strand	18-25	8	34
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	45-51	7	16
β-strand	57-60	4	16
β-strand	68-73	6	34
β-strand	78-83	6	34
α-helix	88-90	3
β-strand	92-99	8	16
β-strand	104-107	4	16
β-strand	109	1	34
β-strand	111-113	3	16
β-strand	114-115	2	35
β-strand	121	1	36
α-helix	122-123	2
β-strand	124-128	5	37
β-strand	140-149	10	37
β-strand	150	1	36
β-strand	155-158	4	38
β-strand	163	1	38
β-strand	167-169	3	37
α-helix	170-172	3
β-strand	173-174	2	37
β-strand	180-188	9	37
β-strand	198-204	7	38
α-helix	205-207	3
β-strand	209-215	7	38

Chains L and O: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	39
β-strand	9-12	4	40
β-strand	18-23	6	39
α-helix	26-30	5
β-strand	35-40	6	40
β-strand	47-50	4	40
β-strand	51	1	41
β-strand	55	1	41
β-strand	64-69	6	39
β-strand	72-77	6	39
α-helix	82-84	3
β-strand	87-92	6	40
β-strand	98-99	2	40
β-strand	103-107	5	40
β-strand	113	1	42
β-strand	116-120	5	43
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	43
β-strand	142	1	42
β-strand	147-152	6	44
β-strand	155-157	3	44
β-strand	161-163	3	43
α-helix	164-166	3
β-strand	167-168	2	43
β-strand	174-182	9	43
α-helix	184-189	6
β-strand	193-199	7	44
β-strand	202-208	7	44

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hepatitis A virus cellular receptor 2	A, B, C, D	protein	110	Homo sapiens	Q8TDQ0 (AlphaFold model)
Fab H	H, I, J, K	protein	229	Homo sapiens
Fab L	L, M, N, O	protein	214	Homo sapiens

Sequence of entity 1 (A, B, C, D), FASTA

>6TXZ_1 Hepatitis A virus cellular receptor 2 (chains A, B, C, D)
MSEVEYRAEVGQNAYLPCFYTPAAPGNLVPVCWGKGACPVFECGNVVLRTDERDVNYWTS
RYWLNGDFRKGDVSLTIENVTLADSGIYCCRIQIPGIMNDEKFNLKLVIK

Sequence of entity 2 (H, I, J, K), FASTA

>6TXZ_2 Fab H (chains H, I, J, K)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISVSGGSTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKANWGFFDYWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAAAHHHHHH

Sequence of entity 3 (L, M, N, O), FASTA

>6TXZ_3 Fab L (chains L, M, N, O)
QSALTQPRSVSGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSKRPSGV
PDRFSGSKSGNTASLTISGLQAEDEADYYCSSYADSVVFGGGTKVTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Identification and characterization of M6903, an antagonistic anti-TIM-3 monoclonal antibody. Zhang, D., Jiang, F., Zaynagetdinov, R. et al. Oncoimmunology (2020) 9:1744921-1744921. DOI 10.1080/2162402X.2020.1744921 · 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…
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)
8TBB 2.5 Å, F9S, novel TIM-3 targeting antibody, bound to IgV domain of TIM-3
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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