Details for 3tyf

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Structure information

Crystal Structure of a CD1D-Lysophosphatidylcholine Reactive inkt TCR

Item	Info
PDB	3tyf
Organism	UNKNOWN
Method	X-RAY DIFFRACTION
Resolution	2.806Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

B / A

TCR Details:

Item	Info
VB chain	B
VA chain	A
VB IMGT details	TRBV25/TRBJ2
VA IMGT details	TRAV10/TRAJ18
Species	human

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	D	I	Y	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
R	Y	L	V	I	G	T	G
B17	B18	B19	B20	B21	B22	B23	B24
K	K	I	T	L	E	C	S
B25	B26	B27	B28	B29	B37	B38	B39
Q	T	M	G	H	D	K	M
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	Q	Q	D	P	G
B48	B49	B50	B51	B52	B53	B54	B55
M	E	L	H	L	I	H	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	Y	G	V	N	S	T	E
B68	B69	B70	B71	B72	B74	B75	B76
K	G	D	L	S	S	E	S
B77	B78	B79	B80	B81	B83	B84	B85
T	V	S	R	I	R	T	E
B86	B87	B88	B89	B90	B91	B92	B93
H	F	P	L	T	L	E	S
B94	B95	B96	B97	B98	B99	B100	B101
A	R	P	S	H	T	S	Q
B102	B103	B104	B105	B106	B107	B108	B109
Y	L	C	A	S	S	E	E
B110	B111	B111A	B112B	B112A	B112	B113	B114
G	A	L	K	E	S	V	G
B115	B116	B117	B118	B119	B120	B121	B122
T	Q	Y	F	G	P	G	T
B123	B124	B125	B126	B127
R	L	L	V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSEEGALKESVGTQY	None	16
CDRB2	SYGVNS	None	6
CDRB1	MGHDK	None	5
CDRA3	VVSDRGSTLGRLY	None	13
CDRA2	MTFSENT	None	7
CDRA1	VSPFSN	None	6

Orientation and docking angles:

Angle	Value
BC2	101.94°
BC1	70.96°
BA	-62.36°
AC2	86.65°
AC1	127.41°
dc	17.27Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2po6_HG	101.02°	70.95°	-61.75°	83.95°	128.24°	17.22Å	3.0
2po6_DC	100.88°	70.51°	-60.85°	85.02°	129.17°	17.22Å	3.1
3tzv_HG	101.12°	70.54°	-61.31°	83.81°	127.17°	17.14Å	3.2
5d7k_ED	101.16°	70.37°	-59.20°	86.27°	126.06°	17.13Å	3.6
6p64_JI	102.94°	73.68°	-61.72°	87.44°	125.40°	16.77Å	3.7

D / C

TCR Details:

Item	Info
VB chain	D
VA chain	C
VB IMGT details	TRBV25/TRBJ2
VA IMGT details	TRAV10/TRAJ18
Species	human

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	D	I	Y	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
R	Y	L	V	I	G	T	G
B17	B18	B19	B20	B21	B22	B23	B24
K	K	I	T	L	E	C	S
B25	B26	B27	B28	B29	B37	B38	B39
Q	T	M	G	H	D	K	M
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	Q	Q	D	P	G
B48	B49	B50	B51	B52	B53	B54	B55
M	E	L	H	L	I	H	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	Y	G	V	N	S	T	E
B68	B69	B70	B71	B72	B74	B75	B76
K	G	D	L	S	S	E	S
B77	B78	B79	B80	B81	B83	B84	B85
T	V	S	R	I	R	T	E
B86	B87	B88	B89	B90	B91	B92	B93
H	F	P	L	T	L	E	S
B94	B95	B96	B97	B98	B99	B100	B101
A	R	P	S	H	T	S	Q
B102	B103	B104	B105	B106	B107	B108	B109
Y	L	C	A	S	S	E	E
B110	B111	B111A	B112B	B112A	B112	B113	B114
G	A	L	K	E	S	V	G
B115	B116	B117	B118	B119	B120	B121	B122
T	Q	Y	F	G	P	G	T
B123	B124	B125	B126	B127
R	L	L	V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSEEGALKESVGTQY	None	16
CDRB2	SYGVNS	None	6
CDRB1	MGHDK	None	5
CDRA3	VVSDRGSTLGRLY	None	13
CDRA2	MTFSENT	None	7
CDRA1	VSPFSN	None	6

Orientation and docking angles:

Angle	Value
BC2	102.08°
BC1	72.13°
BA	-63.97°
AC2	82.92°
AC1	126.43°
dc	16.81Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
3sdx_FE	101.12°	71.44°	-64.76°	81.96°	126.82°	17.19Å	1.8
6ovo_BA	103.01°	72.72°	-64.60°	82.04°	125.37°	16.52Å	1.9
3sdx_HG	100.74°	71.55°	-64.75°	81.91°	126.47°	17.26Å	2.0
4l9l_BA	102.30°	73.18°	-63.63°	80.48°	125.58°	16.78Å	2.8
3he7_DC	102.78°	70.06°	-64.14°	82.60°	124.67°	17.02Å	2.8

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	8.4
3s96_AB	107.61°	73.57°	-66.51°	82.70°	120.78°	16.43Å	8.4
5te6_HL	110.27°	71.02°	-62.37°	82.91°	121.25°	16.49Å	9.9
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	10.0

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