Details for 2eyt

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Structure information

a Structural Basis For Selection and Cross-Species Reactivity of the Semi-invariant Nkt Cell Receptor in CD1D/Glycolipid Recognition

Item	Info
PDB	2eyt
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.6Å
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

B3	B4	B5	B6	B7	B8	B9	B10
D	I	Y	Q	T	P	R	Y
B11	B12	B13	B14	B15	B16	B17	B18
L	V	I	G	T	G	K	K
B19	B20	B21	B22	B23	B24	B25	B26
I	T	L	E	C	S	Q	T
B27	B28	B29	B37	B38	B39	B40	B41
M	G	H	D	K	M	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	Q	Q	D	P	G	M	E
B50	B51	B52	B53	B54	B55	B56	B57
L	H	L	I	H	Y	S	Y
B58	B63	B64	B65	B66	B67	B68	B69
G	V	N	S	T	E	K	G
B70	B71	B72	B74	B75	B76	B77	B78
D	L	S	S	E	S	T	V
B79	B80	B81	B83	B84	B85	B86	B87
S	R	I	R	T	E	H	F
B88	B89	B90	B91	B92	B93	B94	B95
P	L	T	L	E	S	A	R
B96	B97	B98	B99	B100	B101	B102	B103
P	S	H	T	S	Q	Y	L
B104	B105	B106	B107	B108	B109	B110	B111
C	A	S	S	G	L	R	D
B112A	B112	B113	B114	B115	B116	B117	B118
R	G	L	Y	E	Q	Y	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	T	V
B127
T

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	ASSGLRDRGLYEQY	None	14
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	104.12°
BC1	72.35°
BA	-58.29°
AC2	81.38°
AC1	129.49°
dc	16.87Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6rpa_ED	102.31°	73.31°	-58.15°	80.86°	127.64°	17.41Å	2.9
6uln_ED	105.42°	73.24°	-58.64°	84.32°	129.08°	16.84Å	3.4
5ivx_FE	105.11°	70.76°	-57.75°	79.87°	126.86°	17.29Å	3.6
5jzi_JI	103.64°	71.67°	-57.46°	81.83°	125.91°	16.54Å	3.8
6ulr_ED	105.96°	73.47°	-58.86°	84.49°	128.86°	16.82Å	3.9

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	9.0
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	9.3
4hfu_HL	112.36°	71.78°	-58.26°	83.56°	125.23°	16.51Å	9.6
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	9.6
2dtg_CD	112.45°	70.45°	-56.63°	81.76°	125.38°	16.00Å	9.7

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

B3	B4	B5	B6	B7	B8	B9	B10
D	I	Y	Q	T	P	R	Y
B11	B12	B13	B14	B15	B16	B17	B18
L	V	I	G	T	G	K	K
B19	B20	B21	B22	B23	B24	B25	B26
I	T	L	E	C	S	Q	T
B27	B28	B29	B37	B38	B39	B40	B41
M	G	H	D	K	M	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	Q	Q	D	P	G	M	E
B50	B51	B52	B53	B54	B55	B56	B57
L	H	L	I	H	Y	S	Y
B58	B63	B64	B65	B66	B67	B68	B69
G	V	N	S	T	E	K	G
B70	B71	B72	B74	B75	B76	B77	B78
D	L	S	S	E	S	T	V
B79	B80	B81	B83	B84	B85	B86	B87
S	R	I	R	T	E	H	F
B88	B89	B90	B91	B92	B93	B94	B95
P	L	T	L	E	S	A	R
B96	B97	B98	B99	B100	B101	B102	B103
P	S	H	T	S	Q	Y	L
B104	B105	B106	B107	B108	B109	B110	B111
C	A	S	S	G	L	R	D
B112A	B112	B113	B114	B115	B116	B117	B118
R	G	L	Y	E	Q	Y	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	T	V
B127
T

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	ASSGLRDRGLYEQY	None	14
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	104.70°
BC1	70.82°
BA	-53.66°
AC2	83.57°
AC1	132.42°
dc	17.32Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4dzb_BA	105.86°	68.09°	-51.34°	83.86°	131.28°	17.17Å	3.9
2cde_FE	103.80°	70.90°	-51.77°	85.50°	129.72°	17.10Å	3.9
3huj_HG	101.06°	71.26°	-52.04°	84.08°	132.21°	17.27Å	4.0
2cde_DC	103.64°	70.43°	-50.60°	83.45°	129.89°	17.47Å	4.1
3o6f_HG	104.58°	69.75°	-54.07°	87.97°	132.76°	17.81Å	4.6

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