Details for 1nfd

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Structure information

an alpha-Beta T Cell Receptor (TCR) Heterodimer in complex with an anti-TCR Fab Fragment Derived From a Mitogenic antibody

Item	Info
PDB	1nfd
Organism	MUS MUSCULUS
Method	X-RAY DIFFRACTION
Resolution	2.8Å
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	TRBV12/TRBJ2
VA IMGT details	TRAV12/TRAJ40
Species	mouse

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
D	S	G	V	V	Q	S	P
B9	B10	B11	B12	B13	B14	B15	B16
R	H	I	I	K	E	K	G
B17	B18	B19	B20	B21	B22	B23	B24
G	R	S	V	L	T	C	I
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	S	N	V
B40	B41	B42	B43	B44	B45	B46	B47
V	W	Y	Q	Q	T	L	G
B48	B49	B50	B51	B52	B53	B54	B55
K	E	L	K	F	L	I	Q
B56	B57	B58	B63	B64	B65	B66	B67
H	Y	E	K	V	E	R	D
B68	B69	B70	B71	B72	B74	B75	B76
K	G	F	L	P	S	R	F
B77	B78	B79	B80	B81	B83	B84	B85
S	V	Q	Q	F	D	D	Y
B86	B87	B88	B89	B90	B91	B92	B93
H	S	E	M	N	M	S	A
B94	B95	B96	B97	B98	B99	B100	B101
L	E	L	E	D	S	A	M
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	L	R
B110	B113	B114	B115	B116	B117	B118	B119
W	G	D	E	Q	Y	F	G
B120	B121	B122	B123	B124	B125	B126	B127
P	G	T	R	L	T	V	L

FASTA file

A2	A3	A4	A5	A6	A7	A8	A9
D	S	V	T	Q	T	E	G
A10	A11	A12	A13	A14	A15	A16	A17
L	V	T	V	T	E	G	L
A18	A19	A20	A21	A22	A23	A24	A25
P	V	K	L	N	C	T	Y
A26	A27	A28	A29	A30	A36	A37	A38
Q	T	T	Y	L	T	I	A
A39	A40	A41	A42	A43	A44	A45	A46
F	F	W	Y	V	Q	Y	L
A47	A48	A49	A50	A51	A52	A53	A54
N	E	A	P	Q	V	L	L
A55	A56	A57	A58	A59	A63	A64	A65
K	S	S	T	D	N	K	R
A66	A67	A68	A74	A75	A76	A77	A78
T	E	H	Q	G	F	H	A
A79	A80	A81	A82	A83	A84	A85	A86
T	L	H	K	S	S	S	S
A87	A88	A89	A90	A91	A92	A93	A94
F	H	L	Q	K	S	S	A
A95	A96	A97	A98	A99	A100	A101	A102
Q	L	S	D	S	A	L	Y
A103	A104	A105	A106	A107	A108	A109	A110
Y	C	A	L	S	E	G	G
A113	A114	A115	A116	A117	A118	A119	A120
N	Y	K	Y	V	F	G	A
A121	A122	A123	A124	A125	A126	A127
G	T	R	L	K	V	I

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLRWGDEQY	None	11
CDRB2	HYEKVE	None	6
CDRB1	SGHSN	None	5
CDRA3	ALSEGGNYKYV	None	11
CDRA2	SSTDNKR	None	7
CDRA1	TTYLTIA	None	7

Orientation and docking angles:

Angle	Value
BC2	102.62°
BC1	72.94°
BA	-51.39°
AC2	79.73°
AC1	127.94°
dc	16.91Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6vma_ED	100.95°	70.51°	-52.18°	80.98°	126.53°	17.19Å	3.6
6vmc_ED	100.88°	70.42°	-52.90°	80.33°	126.96°	17.14Å	3.6
6py2_ED	106.09°	73.09°	-52.34°	79.71°	126.93°	16.77Å	3.7
4qrp_LK	101.65°	74.60°	-53.08°	81.91°	125.88°	16.97Å	3.9
6vm9_ED	101.11°	71.23°	-53.89°	80.26°	126.06°	16.94Å	3.9

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	8.9
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	8.9
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	9.2
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	9.7

D / C

TCR Details:

Item	Info
VB chain	D
VA chain	C
VB IMGT details	TRBV12/TRBJ2
VA IMGT details	TRAV12/TRAJ40
Species	mouse

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
D	S	G	V	V	Q	S	P
B9	B10	B11	B12	B13	B14	B15	B16
R	H	I	I	K	E	K	G
B17	B18	B19	B20	B21	B22	B23	B24
G	R	S	V	L	T	C	I
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	S	N	V
B40	B41	B42	B43	B44	B45	B46	B47
V	W	Y	Q	Q	T	L	G
B48	B49	B50	B51	B52	B53	B54	B55
K	E	L	K	F	L	I	Q
B56	B57	B58	B63	B64	B65	B66	B67
H	Y	E	K	V	E	R	D
B68	B69	B70	B71	B72	B74	B75	B76
K	G	F	L	P	S	R	F
B77	B78	B79	B80	B81	B83	B84	B85
S	V	Q	Q	F	D	D	Y
B86	B87	B88	B89	B90	B91	B92	B93
H	S	E	M	N	M	S	A
B94	B95	B96	B97	B98	B99	B100	B101
L	E	L	E	D	S	A	M
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	L	R
B110	B113	B114	B115	B116	B117	B118	B119
W	G	D	E	Q	Y	F	G
B120	B121	B122	B123	B124	B125	B126	B127
P	G	T	R	L	T	V	L

FASTA file

A2	A3	A4	A5	A6	A7	A8	A9
D	S	V	T	Q	T	E	G
A10	A11	A12	A13	A14	A15	A16	A17
L	V	T	V	T	E	G	L
A18	A19	A20	A21	A22	A23	A24	A25
P	V	K	L	N	C	T	Y
A26	A27	A28	A29	A30	A36	A37	A38
Q	T	T	Y	L	T	I	A
A39	A40	A41	A42	A43	A44	A45	A46
F	F	W	Y	V	Q	Y	L
A47	A48	A49	A50	A51	A52	A53	A54
N	E	A	P	Q	V	L	L
A55	A56	A57	A58	A59	A63	A64	A65
K	S	S	T	D	N	K	R
A66	A67	A68	A74	A75	A76	A77	A78
T	E	H	Q	G	F	H	A
A79	A80	A81	A82	A83	A84	A85	A86
T	L	H	K	S	S	S	S
A87	A88	A89	A90	A91	A92	A93	A94
F	H	L	Q	K	S	S	A
A95	A96	A97	A98	A99	A100	A101	A102
Q	L	S	D	S	A	L	Y
A103	A104	A105	A106	A107	A108	A109	A110
Y	C	A	L	S	E	G	G
A113	A114	A115	A116	A117	A118	A119	A120
N	Y	K	Y	V	F	G	A
A121	A122	A123	A124	A125	A126	A127
G	T	R	L	K	V	I

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLRWGDEQY	None	11
CDRB2	HYEKVE	None	6
CDRB1	SGHSN	None	5
CDRA3	ALSEGGNYKYV	None	11
CDRA2	SSTDNKR	None	7
CDRA1	TTYLTIA	None	7

Orientation and docking angles:

Angle	Value
BC2	101.71°
BC1	72.76°
BA	-53.95°
AC2	78.25°
AC1	126.45°
dc	16.86Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6vm9_ED	101.11°	71.23°	-53.89°	80.26°	126.06°	16.94Å	2.6
5ksb_HG	100.64°	72.26°	-54.88°	80.22°	125.62°	16.39Å	2.7
5ksb_FE	100.41°	72.25°	-54.96°	79.93°	125.35°	16.44Å	2.7
7ea6_BA	102.15°	75.20°	-54.88°	77.43°	125.68°	16.05Å	3.0
4eup_HG	100.47°	71.36°	-55.50°	80.20°	125.61°	16.91Å	3.2

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	8.8
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	9.2
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	9.4
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	9.5
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	9.6

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