Details for 5til

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Structure information

Murine Class I Major Histocompatibility complex H-2 Db in complex with Lcmv-Derived Gp33 altered Peptide V3P and T-Cell Receptor P14

Item	Info
PDB	5til
Organism	MUS MUSCULUS
Method	X-RAY DIFFRACTION
Resolution	2.83Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

H / G

TCR Details:

Item	Info
VB chain	H
VA chain	G
VB IMGT details	TRBV13/TRBJ2
VA IMGT details	TRAV14/TRAJ48
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	LYMPHOCYTIC CHORIOMENINGITIS MAMMARENAVIRUS
Antigen Sequence	KAPYNFATM
Antigen Length	9

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	mouse
MHC IMGT details	H2-D1b

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B3	B4	B5	B6	B7	B8	B9	B10
A	V	T	Q	S	P	R	S
B11	B12	B13	B14	B15	B16	B17	B18
K	V	A	V	T	G	G	K
B19	B20	B21	B22	B23	B24	B25	B26
V	T	L	S	C	H	Q	T
B27	B28	B29	B37	B38	B39	B40	B41
N	N	H	D	Y	M	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	R	Q	D	T	G	H	G
B50	B51	B52	B53	B54	B55	B56	B57
L	R	L	I	H	Y	S	Y
B58	B63	B64	B65	B66	B67	B68	B69
V	A	D	S	T	E	K	G
B70	B71	B72	B74	B75	B76	B77	B78
D	I	P	D	G	Y	K	A
B79	B80	B81	B83	B84	B85	B86	B87
S	R	P	S	Q	E	N	F
B88	B89	B90	B91	B92	B93	B94	B95
S	L	I	L	E	L	A	S
B96	B97	B98	B99	B100	B101	B102	B103
L	S	Q	T	A	V	Y	F
B104	B105	B106	B107	B108	B109	B110	B112
C	A	S	S	D	A	G	G
B113	B114	B115	B116	B117	B118	B119	B120
R	N	T	L	Y	F	G	A
B121	B122	B123	B124	B125	B126	B127
G	T	R	L	S	V	L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	Q	Q	V	R	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	L	T	V	W	E	G
A17	A18	A19	A20	A21	A22	A23	A24
G	T	T	V	L	T	C	S
A25	A26	A27	A28	A29	A36	A37	A38
Y	E	D	S	T	F	N	Y
A39	A40	A41	A42	A43	A44	A45	A46
F	P	W	Y	Q	Q	F	P
A47	A48	A49	A50	A51	A52	A53	A54
G	E	G	P	A	L	L	I
A55	A56	A57	A58	A59	A63	A64	A65
S	I	L	S	V	S	D	K
A66	A67	A68	A74	A75	A76	A77	A78
K	E	D	G	R	F	T	T
A79	A80	A81	A82	A83	A84	A85	A86
F	F	N	K	R	E	K	K
A87	A88	A89	A90	A91	A92	A93	A94
L	S	L	H	I	I	D	S
A95	A96	A97	A98	A99	A100	A101	A102
Q	P	G	D	S	A	T	Y
A103	A104	A105	A106	A107	A108	A109	A113
F	C	A	A	L	Y	G	N
A114	A115	A116	A117	A118	A119	A120	A121
E	K	I	T	F	G	A	G
A122	A123	A124	A125	A126	A127	A128
T	K	L	T	I	K	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSDAGGRNTLY	None	12
CDRB2	SYVADS	None	6
CDRB1	NNHDY	None	5
CDRA3	AALYGNEKIT	None	10
CDRA2	ILSVSDK	None	7
CDRA1	DSTFNY	None	6

Orientation and docking angles:

Angle	Value
BC2	106.74°
BC1	73.94°
BA	-69.42°
AC2	71.24°
AC1	126.30°
dc	16.57Å
Docking angle	45.16°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5tje_HG	107.04°	73.34°	-68.47°	71.17°	127.35°	16.67Å	1.6
5tje_FE	106.54°	73.15°	-71.52°	69.90°	125.46°	16.62Å	2.8
3mff_DC	107.65°	72.18°	-68.09°	72.85°	125.91°	16.72Å	2.9
5m02_HG	104.84°	73.41°	-67.56°	72.98°	126.46°	16.68Å	3.2
3mff_BA	106.92°	71.88°	-68.46°	73.85°	127.42°	16.76Å	3.6

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	4.9
1jv5_BA	111.45°	73.74°	-67.77°	74.39°	122.07°	15.49Å	7.3
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	8.1
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	9.0
4uim_HL	108.80°	71.21°	-68.16°	75.65°	118.51°	16.05Å	9.7

L / K

TCR Details:

Item	Info
VB chain	L
VA chain	K
VB IMGT details	TRBV13/TRBJ2
VA IMGT details	TRAV14/TRAJ48
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	F
Antigen Type	Peptide
Antigen Organism	LYMPHOCYTIC CHORIOMENINGITIS MAMMARENAVIRUS
Antigen Sequence	KAPYNFATM
Antigen Length	9

MHC details:

Item	Info
MHC Chain	D \| E
MHC Type	MH1
MHC Species	mouse
MHC IMGT details	H2-D1b

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B3	B4	B5	B6	B7	B8	B9	B10
A	V	T	Q	S	P	R	S
B11	B12	B13	B14	B15	B16	B17	B18
K	V	A	V	T	G	G	K
B19	B20	B21	B22	B23	B24	B25	B26
V	T	L	S	C	H	Q	T
B27	B28	B29	B37	B38	B39	B40	B41
N	N	H	D	Y	M	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	R	Q	D	T	G	H	G
B50	B51	B52	B53	B54	B55	B56	B57
L	R	L	I	H	Y	S	Y
B58	B63	B64	B65	B66	B67	B68	B69
V	A	D	S	T	E	K	G
B70	B71	B72	B74	B75	B76	B77	B78
D	I	P	D	G	Y	K	A
B79	B80	B81	B83	B84	B85	B86	B87
S	R	P	S	Q	E	N	F
B88	B89	B90	B91	B92	B93	B94	B95
S	L	I	L	E	L	A	S
B96	B97	B98	B99	B100	B101	B102	B103
L	S	Q	T	A	V	Y	F
B104	B105	B106	B107	B108	B109	B110	B112
C	A	S	S	D	A	G	G
B113	B114	B115	B116	B117	B118	B119	B120
R	N	T	L	Y	F	G	A
B121	B122	B123	B124	B125	B126	B127
G	T	R	L	S	V	L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	Q	Q	V	R	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	L	T	V	W	E	G
A17	A18	A19	A20	A21	A22	A23	A24
G	T	T	V	L	T	C	S
A25	A26	A27	A28	A29	A36	A37	A38
Y	E	D	S	T	F	N	Y
A39	A40	A41	A42	A43	A44	A45	A46
F	P	W	Y	Q	Q	F	P
A47	A48	A49	A50	A51	A52	A53	A54
G	E	G	P	A	L	L	I
A55	A56	A57	A58	A59	A63	A64	A65
S	I	L	S	V	S	D	K
A66	A67	A68	A74	A75	A76	A77	A78
K	E	D	G	R	F	T	T
A79	A80	A81	A82	A83	A84	A85	A86
F	F	N	K	R	E	K	K
A87	A88	A89	A90	A91	A92	A93	A94
L	S	L	H	I	I	D	S
A95	A96	A97	A98	A99	A100	A101	A102
Q	P	G	D	S	A	T	Y
A103	A104	A105	A106	A107	A108	A109	A113
F	C	A	A	L	Y	G	N
A114	A115	A116	A117	A118	A119	A120	A121
E	K	I	T	F	G	A	G
A122	A123	A124	A125	A126	A127	A128
T	K	L	T	I	K	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSDAGGRNTLY	None	12
CDRB2	SYVADS	None	6
CDRB1	NNHDY	None	5
CDRA3	AALYGNEKIT	None	10
CDRA2	ILSVSDK	None	7
CDRA1	DSTFNY	None	6

Orientation and docking angles:

Angle	Value
BC2	106.68°
BC1	73.40°
BA	-71.92°
AC2	69.72°
AC1	124.78°
dc	16.55Å
Docking angle	46.16°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5tje_FE	106.54°	73.15°	-71.52°	69.90°	125.46°	16.62Å	0.9
8trq_ED	104.82°	72.23°	-72.24°	70.19°	123.22°	17.20Å	2.8
7f5k_BA	103.61°	72.42°	-70.38°	68.11°	126.48°	16.45Å	4.3
5tje_HG	107.04°	73.34°	-68.47°	71.17°	127.35°	16.67Å	4.6
3mff_DC	107.65°	72.18°	-68.09°	72.85°	125.91°	16.72Å	5.3

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	4.4
1jv5_BA	111.45°	73.74°	-67.77°	74.39°	122.07°	15.49Å	8.4
12e8_HL	106.48°	69.23°	-70.96°	74.63°	118.60°	16.05Å	9.0
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	9.5
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	9.6

Available downloads

Additional links and files for download: see help for more details.

Item	Link
IMGT-numbered structure	Link
Non-annotated structure from the PDB	Link
Summary file for this TCR	Link
Link in the PDB	Link