Details for 2j8u

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Structure information

Large Cdr3a Loop alteration as a Function of MHC Mutation.

Item	Info
PDB	2j8u
Organism	MUS MUSCULUS
Method	X-RAY DIFFRACTION
Resolution	2.88Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

F / E

TCR Details:

Item	Info
VB chain	F
VA chain	E
VB IMGT details	TRBV13/TRBJ2
VA IMGT details	TRAV12/TRAJ50
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	HOMO SAPIENS
Antigen Sequence	ALWGFFPVL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-A*0201

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
E	A	A	V	T	Q	S	P
B9	B10	B11	B12	B13	B14	B15	B16
R	S	K	V	A	V	T	G
B17	B18	B19	B20	B21	B22	B23	B24
G	K	V	T	L	S	C	H
B25	B26	B27	B28	B29	B37	B38	B39
Q	T	N	N	H	D	Y	M
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	D	T	G
B48	B49	B50	B51	B52	B53	B54	B55
H	G	L	R	L	I	H	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	Y	V	A	D	S	T	E
B68	B69	B70	B71	B72	B74	B75	B76
K	G	D	I	P	D	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
K	A	S	R	P	S	Q	E
B86	B87	B88	B89	B90	B91	B92	B93
N	F	S	L	I	L	E	L
B94	B95	B96	B97	B98	B99	B100	B101
A	S	L	S	Q	T	A	V
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	D	W
B110	B113	B114	B115	B116	B117	B118	B119
V	S	Y	E	Q	Y	F	G
B120	B121	B122	B123	B124	B125	B126	B127
P	G	T	R	L	T	V	L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
M	D	S	V	T	Q	T	E
A9	A10	A11	A12	A13	A14	A15	A16
G	L	V	T	L	T	E	G
A17	A18	A19	A20	A21	A22	A23	A24
L	P	V	M	L	N	C	T
A25	A26	A27	A28	A29	A36	A37	A38
Y	Q	S	T	Y	S	P	F
A39	A40	A41	A42	A43	A44	A45	A46
L	F	W	Y	V	Q	H	L
A47	A48	A49	A50	A51	A52	A53	A54
N	E	A	P	K	L	L	L
A55	A56	A57	A58	A59	A63	A64	A65
K	S	F	T	D	N	K	R
A66	A67	A68	A74	A75	A76	A77	A78
P	E	H	Q	G	F	H	A
A79	A80	A81	A82	A83	A84	A85	A86
T	L	H	K	S	S	S	S
A87	A88	A89	A90	A91	A92	A93	A94
F	H	L	Q	K	S	S	A
A95	A96	A97	A98	A99	A100	A101	A102
Q	L	S	D	S	A	L	Y
A103	A104	A105	A106	A107	A108	A109	A110
Y	C	A	L	F	L	A	S
A111	A112	A113	A114	A115	A116	A117	A118
S	S	F	S	K	L	V	F
A119	A120	A121	A122	A123	A124	A125	A126
G	Q	G	T	S	L	S	V
A127	A128
V	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSDWVSYEQY	None	11
CDRB2	SYVADS	None	6
CDRB1	NNHDY	None	5
CDRA3	ALFLASSSFSKLV	A3-13-D	13
CDRA2	SFTDNKR	None	7
CDRA1	STYSPF	None	6

Orientation and docking angles:

Angle	Value
BC2	108.31°
BC1	74.02°
BA	-66.29°
AC2	74.42°
AC1	123.85°
dc	16.69Å
Docking angle	68.88°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
1lp9_FE	108.68°	73.78°	-66.70°	74.14°	123.92°	16.54Å	0.7
2uwe_FE	109.04°	74.17°	-66.62°	74.12°	124.21°	16.65Å	0.9
1lp9_ML	108.14°	73.36°	-66.36°	74.25°	124.79°	16.60Å	1.2
2jcc_FE	109.08°	74.58°	-66.28°	75.05°	124.04°	16.62Å	1.2
2uwe_ML	108.04°	73.37°	-66.20°	73.74°	124.87°	16.70Å	1.4

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1jv5_BA	111.45°	73.74°	-67.77°	74.39°	122.07°	15.49Å	4.1
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	4.7
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	5.4
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	6.2
3wih_IM	112.74°	73.69°	-62.39°	76.91°	120.77°	15.54Å	7.2

M / L

TCR Details:

Item	Info
VB chain	M
VA chain	L
VB IMGT details	TRBV13/TRBJ2
VA IMGT details	TRAV12/TRAJ50
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	J
Antigen Type	Peptide
Antigen Organism	HOMO SAPIENS
Antigen Sequence	ALWGFFPVL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	H \| I
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-A*0201

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
E	A	A	V	T	Q	S	P
B9	B10	B11	B12	B13	B14	B15	B16
R	S	K	V	A	V	T	G
B17	B18	B19	B20	B21	B22	B23	B24
G	K	V	T	L	S	C	H
B25	B26	B27	B28	B29	B37	B38	B39
Q	T	N	N	H	D	Y	M
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	D	T	G
B48	B49	B50	B51	B52	B53	B54	B55
H	G	L	R	L	I	H	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	Y	V	A	D	S	T	E
B68	B69	B70	B71	B72	B74	B75	B76
K	G	D	I	P	D	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
K	A	S	R	P	S	Q	E
B86	B87	B88	B89	B90	B91	B92	B93
N	F	S	L	I	L	E	L
B94	B95	B96	B97	B98	B99	B100	B101
A	S	L	S	Q	T	A	V
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	D	W
B110	B113	B114	B115	B116	B117	B118	B119
V	S	Y	E	Q	Y	F	G
B120	B121	B122	B123	B124	B125	B126	B127
P	G	T	R	L	T	V	L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
M	D	S	V	T	Q	T	E
A9	A10	A11	A12	A13	A14	A15	A16
G	L	V	T	L	T	E	G
A17	A18	A19	A20	A21	A22	A23	A24
L	P	V	M	L	N	C	T
A25	A26	A27	A28	A29	A36	A37	A38
Y	Q	S	T	Y	S	P	F
A39	A40	A41	A42	A43	A44	A45	A46
L	F	W	Y	V	Q	H	L
A47	A48	A49	A50	A51	A52	A53	A54
N	E	A	P	K	L	L	L
A55	A56	A57	A58	A59	A63	A64	A65
K	S	F	T	D	N	K	R
A66	A67	A68	A74	A75	A76	A77	A78
P	E	H	Q	G	F	H	A
A79	A80	A81	A82	A83	A84	A85	A86
T	L	H	K	S	S	S	S
A87	A88	A89	A90	A91	A92	A93	A94
F	H	L	Q	K	S	S	A
A95	A96	A97	A98	A99	A100	A101	A102
Q	L	S	D	S	A	L	Y
A103	A104	A105	A106	A107	A108	A109	A110
Y	C	A	L	F	L	A	S
A111	A112	A113	A114	A115	A116	A117	A118
S	S	F	S	K	L	V	F
A119	A120	A121	A122	A123	A124	A125	A126
G	Q	G	T	S	L	S	V
A127	A128
V	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSDWVSYEQY	None	11
CDRB2	SYVADS	None	6
CDRB1	NNHDY	None	5
CDRA3	ALFLASSSFSKLV	A3-13-D	13
CDRA2	SFTDNKR	None	7
CDRA1	STYSPF	None	6

Orientation and docking angles:

Angle	Value
BC2	107.93°
BC1	72.98°
BA	-66.36°
AC2	73.99°
AC1	124.42°
dc	16.81Å
Docking angle	66.04°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
1lp9_ML	108.14°	73.36°	-66.36°	74.25°	124.79°	16.60Å	0.7
2uwe_ML	108.04°	73.37°	-66.20°	73.74°	124.87°	16.70Å	0.7
1lp9_FE	108.68°	73.78°	-66.70°	74.14°	123.92°	16.54Å	1.3
2z31_BA	107.66°	72.97°	-66.65°	73.04°	123.84°	16.30Å	1.3
2pxy_BA	107.69°	72.09°	-67.17°	74.08°	123.73°	16.39Å	1.5

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	4.5
1jv5_BA	111.45°	73.74°	-67.77°	74.39°	122.07°	15.49Å	4.7
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	5.5
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	6.2
4uil_HL	109.73°	69.62°	-65.41°	77.88°	119.52°	16.24Å	7.4

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