Details for 4e42

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Structure information

Structural Basis For the Recognition of Mutant Self By a Tumor-Specific, MHC Class Ii-Restricted T Cell Receptor G4

Item	Info
PDB	4e42
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.7Å
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	TRBV5/TRBJ2
VA IMGT details	TRAV22/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
G	V	T	Q	S	P	T	H
B11	B12	B13	B14	B15	B16	B17	B18
L	I	K	T	R	G	Q	Q
B19	B20	B21	B22	B23	B24	B25	B26
A	T	L	R	C	S	P	I
B27	B28	B29	B37	B38	B39	B40	B41
S	G	H	T	S	V	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	Q	Q	A	L	G	L	G
B50	B51	B52	B53	B54	B55	B56	B57
L	Q	F	L	L	W	Y	D
B58	B63	B64	B65	B66	B67	B68	B69
E	G	E	E	R	N	R	G
B70	B71	B72	B74	B75	B76	B77	B78
N	F	P	P	R	F	S	G
B79	B80	B81	B83	B84	B85	B86	B87
R	Q	F	P	N	Y	S	S
B88	B89	B90	B91	B92	B93	B94	B95
E	L	N	V	N	A	L	E
B96	B97	B98	B99	B100	B101	B102	B103
L	E	D	S	A	L	Y	L
B104	B105	B106	B107	B108	B109	B113	B114
C	A	S	S	Q	I	R	E
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

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSQIRETQY	None	10
CDRB2	YDEGEE	None	6
CDRB1	SGHTS	None	5
CDRA3	AVDRGSTLGRLY	None	12
CDRA2	IPSGT	None	5
CDRA1	DSVNN	A1-5-B	5

Orientation and docking angles:

Angle	Value
BC2	100.75°
BC1	70.98°
BA	-53.41°
AC2	81.65°
AC1	121.31°
dc	16.13Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
7pdx_BA	101.38°	72.06°	-55.01°	82.98°	122.29°	16.58Å	2.7
4jfh_ED	100.12°	72.76°	-55.04°	82.61°	121.25°	15.95Å	2.7
6mss_BA	101.09°	73.12°	-55.20°	81.96°	121.34°	16.03Å	2.8
6mra_BA	100.44°	73.77°	-54.63°	82.11°	122.00°	15.88Å	3.2
7pdx_DC	102.41°	72.11°	-55.33°	83.01°	122.30°	16.41Å	3.3

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	6.5
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	7.7
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	8.0
1cft_BA	107.61°	67.68°	-51.49°	84.71°	119.99°	16.31Å	8.5
3mnv_DC	108.94°	70.99°	-55.77°	82.75°	119.97°	16.56Å	8.7

D / C

TCR Details:

Item	Info
VB chain	D
VA chain	C
VB IMGT details	TRBV5/TRBJ2
VA IMGT details	TRAV22/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
G	V	T	Q	S	P	T	H
B11	B12	B13	B14	B15	B16	B17	B18
L	I	K	T	R	G	Q	Q
B19	B20	B21	B22	B23	B24	B25	B26
A	T	L	R	C	S	P	I
B27	B28	B29	B37	B38	B39	B40	B41
S	G	H	T	S	V	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	Q	Q	A	L	G	L	G
B50	B51	B52	B53	B54	B55	B56	B57
L	Q	F	L	L	W	Y	D
B58	B63	B64	B65	B66	B67	B68	B69
E	G	E	E	R	N	R	G
B70	B71	B72	B74	B75	B76	B77	B78
N	F	P	P	R	F	S	G
B79	B80	B81	B83	B84	B85	B86	B87
R	Q	F	P	N	Y	S	S
B88	B89	B90	B91	B92	B93	B94	B95
E	L	N	V	N	A	L	E
B96	B97	B98	B99	B100	B101	B102	B103
L	E	D	S	A	L	Y	L
B104	B105	B106	B107	B108	B109	B113	B114
C	A	S	S	Q	I	R	E
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

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSQIRETQY	None	10
CDRB2	YDEGEE	None	6
CDRB1	SGHTS	None	5
CDRA3	AVDRGSTLGRLY	None	12
CDRA2	IPSGT	None	5
CDRA1	DSVNN	A1-5-B	5

Orientation and docking angles:

Angle	Value
BC2	101.69°
BC1	69.47°
BA	-52.06°
AC2	81.97°
AC1	124.55°
dc	16.37Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
1ao7_ED	101.22°	70.44°	-53.35°	82.76°	124.53°	17.28Å	2.1
1qrn_ED	100.87°	70.09°	-53.19°	83.07°	125.46°	17.07Å	2.2
1qsf_ED	100.59°	70.43°	-53.95°	81.96°	125.01°	16.83Å	2.5
6vma_ED	100.95°	70.51°	-52.18°	80.98°	126.53°	17.19Å	2.7
1qse_ED	100.14°	70.59°	-54.40°	82.15°	125.25°	17.00Å	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	6.6
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	7.6
1cft_BA	107.61°	67.68°	-51.49°	84.71°	119.99°	16.31Å	8.2
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	8.6
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	8.6

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