Details for 7pdx

Click on any of the tabs below to see the detailed information about the structure.

Structure visualisation

Display options:
Cartoon model
Spacefill model
Wire model
Ball&stick model
Default colouring
Color by B-factor
Color by chain
Color by sec. structure
Color by element
Spin: on off

Structure information

Crystal Structure of Parent Mage-a10 TCR (728)

Item	Info
PDB	7pdx
Organism	SYNTHETIC CONSTRUCT
Method	X-RAY DIFFRACTION
Resolution	2.27Å
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	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ5
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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	R	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	L	C	A
B25	B26	B27	B28	B29	B37	B38	B39
Q	D	M	N	H	E	Y	M
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	D	P	G
B48	B49	B50	B51	B52	B53	B54	B55
M	G	L	R	L	I	H	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	V	G	E	G	T	T	A
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	D	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	L	K	K	Q
B86	B87	B88	B89	B90	B91	B92	B93
N	F	L	L	G	L	E	S
B94	B95	B96	B97	B98	B99	B100	B101
A	A	P	S	Q	T	S	V
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	F	T
B114	B115	B116	B117	B118	B119	B120	B121
D	T	Q	Y	F	G	P	G
B122	B123	B124	B125	B126	B127
T	R	L	T	V	L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	K	E	V	E	Q	N	S
A9	A10	A11	A12	A13	A14	A15	A16
G	P	L	S	V	P	E	G
A17	A18	A19	A20	A21	A22	A23	A24
A	I	A	S	L	N	C	T
A25	A26	A27	A28	A29	A36	A37	A38
Y	S	D	R	G	S	Q	S
A39	A40	A41	A42	A43	A44	A45	A46
F	F	W	Y	R	Q	Y	S
A47	A48	A49	A50	A51	A52	A53	A54
G	K	S	P	E	L	I	M
A55	A56	A57	A58	A63	A64	A65	A66
S	I	Y	S	N	G	D	K
A67	A68	A74	A75	A76	A77	A78	A79
E	D	G	R	F	T	A	Q
A80	A81	A82	A83	A84	A85	A86	A87
L	N	K	A	S	Q	Y	V
A88	A89	A90	A91	A92	A93	A94	A95
S	L	L	I	R	D	S	Q
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	S	A	T	Y	L
A104	A105	A106	A107	A108	A109	A110	A113
C	A	V	R	G	T	G	R
A114	A115	A116	A117	A118	A119	A120	A121
R	A	L	T	F	G	S	G
A122	A123	A124	A125	A126	A127	A128
T	R	L	Q	V	Q	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSFTDTQY	None	9
CDRB2	SVGEGT	None	6
CDRB1	MNHEY	None	5
CDRA3	AVRGTGRRALT	None	11
CDRA2	IYSNGD	None	6
CDRA1	DRGSQS	None	6

Orientation and docking angles:

Angle	Value
BC2	101.38°
BC1	72.06°
BA	-55.01°
AC2	82.98°
AC1	122.29°
dc	16.58Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4jfh_ED	100.12°	72.76°	-55.04°	82.61°	121.25°	15.95Å	1.9
6mss_BA	101.09°	73.12°	-55.20°	81.96°	121.34°	16.03Å	1.9
6mra_BA	100.44°	73.77°	-54.63°	82.11°	122.00°	15.88Å	2.3
3vxs_ED	100.98°	72.92°	-55.61°	83.05°	120.18°	15.92Å	2.5
7fjd_nm	101.57°	73.15°	-55.98°	81.85°	123.90°	17.77Å	2.7

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	6.1
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	7.4
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	8.0
3mnv_DC	108.94°	70.99°	-55.77°	82.75°	119.97°	16.56Å	8.0
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	8.1

D / C

TCR Details:

Item	Info
VB chain	D
VA chain	C
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ5
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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	R	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	L	C	A
B25	B26	B27	B28	B29	B37	B38	B39
Q	D	M	N	H	E	Y	M
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	D	P	G
B48	B49	B50	B51	B52	B53	B54	B55
M	G	L	R	L	I	H	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	V	G	E	G	T	T	A
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	D	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	L	K	K	Q
B86	B87	B88	B89	B90	B91	B92	B93
N	F	L	L	G	L	E	S
B94	B95	B96	B97	B98	B99	B100	B101
A	A	P	S	Q	T	S	V
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	F	T
B114	B115	B116	B117	B118	B119	B120	B121
D	T	Q	Y	F	G	P	G
B122	B123	B124	B125	B126	B127
T	R	L	T	V	L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	K	E	V	E	Q	N	S
A9	A10	A11	A12	A13	A14	A15	A16
G	P	L	S	V	P	E	G
A17	A18	A19	A20	A21	A22	A23	A24
A	I	A	S	L	N	C	T
A25	A26	A27	A28	A29	A36	A37	A38
Y	S	D	R	G	S	Q	S
A39	A40	A41	A42	A43	A44	A45	A46
F	F	W	Y	R	Q	Y	S
A47	A48	A49	A50	A51	A52	A53	A54
G	K	S	P	E	L	I	M
A55	A56	A57	A58	A63	A64	A65	A66
S	I	Y	S	N	G	D	K
A67	A68	A74	A75	A76	A77	A78	A79
E	D	G	R	F	T	A	Q
A80	A81	A82	A83	A84	A85	A86	A87
L	N	K	A	S	Q	Y	V
A88	A89	A90	A91	A92	A93	A94	A95
S	L	L	I	R	D	S	Q
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	S	A	T	Y	L
A104	A105	A106	A107	A108	A109	A110	A113
C	A	V	R	G	T	G	R
A114	A115	A116	A117	A118	A119	A120	A121
R	A	L	T	F	G	S	G
A122	A123	A124	A125	A126	A127	A128
T	R	L	Q	V	Q	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSFTDTQY	None	9
CDRB2	SVGEGT	None	6
CDRB1	MNHEY	None	5
CDRA3	AVRGTGRRALT	None	11
CDRA2	IYSNGD	None	6
CDRA1	DRGSQS	None	6

Orientation and docking angles:

Angle	Value
BC2	102.41°
BC1	72.11°
BA	-55.33°
AC2	83.01°
AC1	122.30°
dc	16.41Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6mss_BA	101.09°	73.12°	-55.20°	81.96°	121.34°	16.03Å	2.2
7nmf_ED	102.41°	74.13°	-54.73°	81.83°	121.62°	16.17Å	2.5
4udu_BA	102.41°	72.02°	-57.03°	81.05°	122.79°	15.65Å	2.7
3vxs_ED	100.98°	72.92°	-55.61°	83.05°	120.18°	15.92Å	2.7
4jfh_ED	100.12°	72.76°	-55.04°	82.61°	121.25°	15.95Å	2.7

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	5.3
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	6.5
3mnv_DC	108.94°	70.99°	-55.77°	82.75°	119.97°	16.56Å	7.0
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	7.1
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	7.4

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