Details for 2cde

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Structure information

Structure and Binding Kinetics of Three Different Human CD1D-alpha- Galactosylceramide Specific T Cell Receptors - inkt-TCR

Item	Info
PDB	2cde
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	3.5Å
Number of TCRs	3

Paired chains information

This PDB has 3 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	N
B110	B111	B112	B113	B114	B115	B116	B117
I	G	T	A	Y	E	Q	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	T
B126	B127
V	T

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSENIGTAYEQY	None	13
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	102.73°
BC1	68.97°
BA	-51.15°
AC2	85.99°
AC1	130.58°
dc	17.61Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4pj8_DC	103.12°	69.08°	-49.98°	85.22°	131.61°	17.49Å	1.8
3huj_HG	101.06°	71.26°	-52.04°	84.08°	132.21°	17.27Å	3.9
4dzb_BA	105.86°	68.09°	-51.34°	83.86°	131.28°	17.17Å	4.0
2eys_BA	105.18°	68.91°	-48.08°	87.29°	132.33°	17.71Å	4.5
3o6f_HG	104.58°	69.75°	-54.07°	87.97°	132.76°	17.81Å	4.6

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	N
B110	B111	B112	B113	B114	B115	B116	B117
I	G	T	A	Y	E	Q	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	T
B126	B127
V	T

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSENIGTAYEQY	None	13
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	103.64°
BC1	70.43°
BA	-50.60°
AC2	83.45°
AC1	129.89°
dc	17.47Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4pj8_DC	103.12°	69.08°	-49.98°	85.22°	131.61°	17.49Å	2.9
3vxt_BA	105.58°	68.21°	-50.00°	82.91°	128.68°	17.61Å	3.3
4dzb_BA	105.86°	68.09°	-51.34°	83.86°	131.28°	17.17Å	3.6
3vxt_DC	105.54°	68.24°	-49.02°	82.96°	128.68°	17.67Å	3.6
3huj_HG	101.06°	71.26°	-52.04°	84.08°	132.21°	17.27Å	3.9

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	9.5
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	9.6
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	10.0

F / E

TCR Details:

Item	Info
VB chain	F
VA chain	E
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	N
B110	B111	B112	B113	B114	B115	B116	B117
I	G	T	A	Y	E	Q	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	T
B126	B127
V	T

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSENIGTAYEQY	None	13
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	103.80°
BC1	70.90°
BA	-51.77°
AC2	85.50°
AC1	129.72°
dc	17.10Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4pj8_DC	103.12°	69.08°	-49.98°	85.22°	131.61°	17.49Å	3.3
2eyt_DC	104.70°	70.82°	-53.66°	83.57°	132.42°	17.32Å	3.9
3huj_HG	101.06°	71.26°	-52.04°	84.08°	132.21°	17.27Å	4.0
4onh_BA	106.40°	71.96°	-51.81°	87.71°	127.93°	17.28Å	4.0
4dzb_BA	105.86°	68.09°	-51.34°	83.86°	131.28°	17.17Å	4.2

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	8.5
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	9.4
4qth_AB	111.26°	70.26°	-51.98°	83.39°	123.62°	16.07Å	9.9

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