Details for 4y2d

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Structure information

Crystal Structure of the MCD1D/7Dw8-5/inkTCR Ternary complex

Item	Info
PDB	4y2d
Organism	CHIMERIC HOMO SAPIENS/MUS MUSCULUS
Method	X-RAY DIFFRACTION
Resolution	3.05Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

D / C

TCR Details:

Item	Info
VB chain	D
VA chain	C
VB IMGT details	TRBV13/TRBJ2
VA IMGT details	TRAV11/TRAJ18
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	A
Antigen Type	Hapten
Antigen Organism	MUS MUSCULUS
Antigen name	11-(4-fluorophenyl)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide
Antigen residue	7DW

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	CD1
MHC Species	mouse
MHC IMGT details	CD1D1*01

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	N	K	V	A	V	T	G
B17	B18	B19	B20	B21	B22	B23	B24
G	K	V	T	L	S	C	N
B25	B26	B27	B28	B29	B37	B38	B39
Q	T	N	N	H	N	N	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	G	A	G	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	T	P	S	Q	T	S	V
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	G	D	E
B113	B114	B115	B116	B117	B118	B119	B120
G	Y	T	Q	Y	F	G	P
B121	B122	B123	B124	B125	B126	B127
G	T	R	L	L	V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASGDEGYTQY	None	10
CDRB2	SYGAGS	None	6
CDRB1	NNHNN	None	5
CDRA3	VVGDRGSALGRLH	None	13
CDRA2	LVDQKDK	A2-7-C	7
CDRA1	VTPDNH	None	6

Orientation and docking angles:

Angle	Value
BC2	99.26°
BC1	78.05°
BA	-59.53°
AC2	79.02°
AC1	122.49°
dc	16.22Å
Docking angle	26.84°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4y4f_HG	99.45°	78.23°	-59.68°	79.07°	122.51°	16.15Å	0.3
6miy_HG	99.40°	78.41°	-59.07°	78.95°	122.80°	16.20Å	0.7
6mja_DC	99.40°	78.37°	-58.78°	78.90°	122.84°	16.17Å	0.9
4y4h_DC	99.92°	78.02°	-59.31°	79.27°	123.06°	16.36Å	0.9
3o9w_DC	99.29°	77.76°	-59.52°	79.49°	123.22°	16.28Å	0.9

H / G

TCR Details:

Item	Info
VB chain	H
VA chain	G
VB IMGT details	TRBV13/TRBJ2
VA IMGT details	TRAV11/TRAJ18
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	E
Antigen Type	Hapten
Antigen Organism	MUS MUSCULUS
Antigen name	11-(4-fluorophenyl)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide
Antigen residue	7DW

MHC details:

Item	Info
MHC Chain	E \| F
MHC Type	CD1
MHC Species	mouse
MHC IMGT details	CD1D1*01

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	N	K	V	A	V	T	G
B17	B18	B19	B20	B21	B22	B23	B24
G	K	V	T	L	S	C	N
B25	B26	B27	B28	B29	B37	B38	B39
Q	T	N	N	H	N	N	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	G	A	G	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	T	P	S	Q	T	S	V
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	G	D	E
B113	B114	B115	B116	B117	B118	B119	B120
G	Y	T	Q	Y	F	G	P
B121	B122	B123	B124	B125	B126	B127
G	T	R	L	L	V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASGDEGYTQY	None	10
CDRB2	SYGAGS	None	6
CDRB1	NNHNN	None	5
CDRA3	VVGDRGSALGRLH	None	13
CDRA2	LVDQKDK	A2-7-C	7
CDRA1	VTPDNH	None	6

Orientation and docking angles:

Angle	Value
BC2	98.84°
BC1	78.31°
BA	-57.93°
AC2	79.70°
AC1	122.33°
dc	16.26Å
Docking angle	25.20°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4y4f_DC	98.87°	78.73°	-57.84°	79.54°	122.30°	16.12Å	0.5
6bnk_HG	99.22°	78.94°	-57.78°	79.39°	122.30°	16.15Å	0.8
6cw9_DC	99.40°	78.65°	-57.87°	79.12°	122.47°	16.13Å	0.9
6cwb_DC	99.58°	78.71°	-57.99°	79.33°	122.49°	16.11Å	0.9
4y4h_HG	98.91°	78.34°	-58.46°	79.04°	122.60°	16.35Å	0.9

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