Details for 8vd0

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Structure information

Human TCR Et650-4 in complex with Dq8-insc8-15-Iapp2

Item	Info
PDB	8vd0
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.4Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

E / D

TCR Details:

Item	Info
VB chain	E
VA chain	D
VB IMGT details	TRBV5/TRBJ1
VA IMGT details	TRAV26/TRAJ42
Species	human

MHC details:

Item	Info
MHC Chain	A \| C
MHC Type	MH2
MHC Species	human
MHC IMGT details	HLA-DQA10301 / HLA-DQB10302

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

A3	A4	A5	A6	A8	A9	A10	A11
K	T	T	Q	P	P	S	M
A12	A13	A14	A15	A16	A17	A18	A19
D	C	A	E	G	R	A	A
A20	A21	A22	A23	A24	A25	A26	A27
N	L	P	C	N	H	S	T
A28	A29	A30	A36	A37	A38	A39	A40
I	S	G	N	E	Y	V	Y
A41	A42	A43	A44	A45	A46	A47	A48
W	Y	R	Q	I	H	S	Q
A49	A50	A51	A52	A53	A54	A55	A56
G	P	Q	Y	I	I	H	G
A57	A58	A64	A65	A66	A67	A68	A74
L	K	N	N	E	T	N	E
A75	A76	A77	A78	A79	A80	A81	A82
M	A	S	L	I	I	T	E
A83	A84	A85	A86	A87	A88	A89	A90
D	R	K	S	S	T	L	I
A91	A92	A93	A94	A95	A96	A97	A98
L	P	H	A	T	L	R	D
A99	A100	A101	A102	A103	A104	A105	A106
T	A	V	Y	Y	C	I	V
A107	A108	A109	A110	A111	A112A	A112	A113
R	V	A	I	E	G	S	Q
A114	A115	A116	A117	A118	A119	A120	A121
G	N	L	I	F	G	K	G
A122	A123	A124	A125	A126	A127	A128
T	K	L	S	V	K	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLRRGDTIY	None	11
CDRB2	YFSETQ	None	6
CDRB1	SGHRS	None	5
CDRA3	IVRVAIEGSQGNLI	None	14
CDRA2	GLKNN	None	5
CDRA1	TISGNEY	None	7

Orientation and docking angles:

Angle	Value
BC2	108.62°
BC1	70.83°
BA	-54.02°
AC2	95.19°
AC1	131.05°
dc	17.35Å
Docking angle	39.30°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
8vd2_ED	108.51°	70.82°	-55.99°	93.57°	129.47°	17.24Å	3.0
4gg8_FE	107.56°	70.66°	-50.66°	94.18°	132.57°	17.45Å	4.0
4gg8_BA	107.54°	70.62°	-50.55°	94.37°	132.63°	17.48Å	4.1
7dzm_DE	104.92°	71.39°	-51.44°	93.90°	130.79°	17.55Å	4.7
7dzn_DE	104.31°	71.30°	-51.03°	94.04°	131.03°	17.63Å	5.4

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV5/TRBJ1
VA IMGT details	TRAV26/TRAJ42
Species	human

MHC details:

Item	Info
MHC Chain	F \| H
MHC Type	MH2
MHC Species	human
MHC IMGT details	HLA-DQA10301 / HLA-DQB10302

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

A3	A4	A5	A6	A8	A9	A10	A11
K	T	T	Q	P	P	S	M
A12	A13	A14	A15	A16	A17	A18	A19
D	C	A	E	G	R	A	A
A20	A21	A22	A23	A24	A25	A26	A27
N	L	P	C	N	H	S	T
A28	A29	A30	A36	A37	A38	A39	A40
I	S	G	N	E	Y	V	Y
A41	A42	A43	A44	A45	A46	A47	A48
W	Y	R	Q	I	H	S	Q
A49	A50	A51	A52	A53	A54	A55	A56
G	P	Q	Y	I	I	H	G
A57	A58	A64	A65	A66	A67	A68	A74
L	K	N	N	E	T	N	E
A75	A76	A77	A78	A79	A80	A81	A82
M	A	S	L	I	I	T	E
A83	A84	A85	A86	A87	A88	A89	A90
D	R	K	S	S	T	L	I
A91	A92	A93	A94	A95	A96	A97	A98
L	P	H	A	T	L	R	D
A99	A100	A101	A102	A103	A104	A105	A106
T	A	V	Y	Y	C	I	V
A107	A108	A109	A110	A111	A112A	A112	A113
R	V	A	I	E	G	S	Q
A114	A115	A116	A117	A118	A119	A120	A121
G	N	L	I	F	G	K	G
A122	A123	A124	A125	A126	A127	A128
T	K	L	S	V	K	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLRRGDTIY	None	11
CDRB2	YFSETQ	None	6
CDRB1	SGHRS	None	5
CDRA3	IVRVAIEGSQGNLI	None	14
CDRA2	GLKNN	None	5
CDRA1	TISGNEY	None	7

Orientation and docking angles:

Angle	Value
BC2	108.28°
BC1	71.33°
BA	-55.14°
AC2	93.60°
AC1	129.38°
dc	17.32Å
Docking angle	39.10°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
8vd2_ED	108.51°	70.82°	-55.99°	93.57°	129.47°	17.24Å	1.0
3pqy_JI	107.68°	69.73°	-56.20°	90.17°	132.20°	18.07Å	4.9
3pqy_ON	107.82°	69.20°	-57.40°	90.47°	131.73°	18.14Å	5.1
7dzm_DE	104.92°	71.39°	-51.44°	93.90°	130.79°	17.55Å	5.2
3pqy_TS	105.91°	69.89°	-57.66°	90.05°	131.38°	18.13Å	5.6

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4jpw_HL	112.65°	71.66°	-58.66°	89.39°	123.36°	16.92Å	9.3
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	9.8
2w60_AB	111.29°	72.16°	-56.81°	86.34°	123.74°	16.34Å	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