Details for 3dxa

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 the Dm1 TCR in complex with HLA-B*4405 and Decamer Ebv antigen

Item	Info
PDB	3dxa
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	3.5Å
Number of TCRs	3

Paired chains information

This PDB has 3 TCR(s).

E / D

TCR Details:

Item	Info
VB chain	E
VA chain	D
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV26/TRAJ13
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	EENLLDFVRF
Antigen Length	10

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*4405

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B2	B3	B4	B5	B6	B7	B8	B9
T	G	V	S	Q	N	P	R
B10	B11	B12	B13	B14	B15	B16	B17
H	K	I	T	K	R	G	Q
B18	B19	B20	B21	B22	B23	B24	B25
N	V	T	F	R	C	D	P
B26	B27	B28	B29	B37	B38	B39	B40
I	S	E	H	N	R	L	Y
B41	B42	B43	B44	B45	B46	B47	B48
W	Y	R	Q	T	L	G	Q
B49	B50	B51	B52	B53	B54	B55	B56
G	P	E	F	L	T	Y	F
B57	B58	B63	B64	B65	B66	B67	B68
Q	N	E	A	Q	L	E	K
B69	B70	B71	B72	B73	B74	B75	B76
S	R	L	L	S	D	R	F
B77	B78	B79	B80	B81	B83	B84	B85
S	A	E	R	P	K	G	S
B86	B87	B88	B89	B90	B91	B92	B93
F	S	T	L	E	I	Q	R
B94	B95	B96	B97	B98	B99	B100	B101
T	E	Q	G	D	S	A	M
B102	B103	B104	B105	B106	B107	B108	B109
Y	L	C	A	S	R	Y	R
B110	B111	B112	B113	B114	B115	B116	B117
D	D	S	Y	N	E	Q	F
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	T
B126	B127
V	L

FASTA file

A2	A3	A4	A5	A6	A8	A9	A10
A	K	T	T	Q	P	T	S
A11	A12	A13	A14	A15	A16	A17	A18
M	D	C	A	E	G	R	A
A19	A20	A21	A22	A23	A24	A25	A26
A	N	L	P	C	N	H	S
A27	A28	A29	A30	A36	A37	A38	A39
T	I	S	G	N	E	Y	V
A40	A41	A42	A43	A44	A45	A46	A47
Y	W	Y	R	Q	I	H	S
A48	A49	A50	A51	A52	A53	A54	A55
Q	G	P	Q	Y	I	I	H
A56	A57	A58	A64	A65	A66	A67	A68
G	L	K	N	N	E	T	N
A74	A75	A76	A77	A78	A79	A80	A81
E	M	A	S	L	I	I	T
A82	A83	A84	A85	A86	A87	A88	A89
E	D	R	K	S	S	T	L
A90	A91	A92	A93	A94	A95	A96	A97
I	L	P	H	A	T	L	R
A98	A99	A100	A101	A102	A103	A104	A105
D	T	A	V	Y	Y	C	I
A106	A107	A108	A109	A113	A114	A115	A116
V	W	G	G	Y	Q	K	V
A117	A118	A119	A120	A121	A122	A123	A124
T	F	G	T	G	T	K	L
A125	A126	A127	A128
Q	V	I	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASRYRDDSYNEQF	None	13
CDRB2	FQNEAQ	None	6
CDRB1	SEHNR	None	5
CDRA3	IVWGGYQKVT	None	10
CDRA2	GLKNN	None	5
CDRA1	TISGNEY	None	7

Orientation and docking angles:

Angle	Value
BC2	112.24°
BC1	72.38°
BA	-62.37°
AC2	87.77°
AC1	130.29°
dc	18.02Å
Docking angle	58.06°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4gg6_FE	111.17°	73.07°	-62.86°	89.77°	131.55°	16.94Å	2.9
6avg_DC	111.12°	74.76°	-63.24°	87.80°	129.13°	17.03Å	3.2
4gg6_HG	110.99°	73.29°	-63.02°	90.06°	131.30°	16.97Å	3.2
1kgc_ED	109.35°	71.85°	-63.15°	86.71°	130.57°	17.26Å	3.3
1mi5_ED	109.30°	72.73°	-63.43°	87.70°	131.17°	17.09Å	3.4

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4xvs_HL	115.53°	75.40°	-59.24°	84.30°	126.77°	16.08Å	7.6
4hfu_HL	112.36°	71.78°	-58.26°	83.56°	125.23°	16.51Å	7.9
4s1q_HL	115.45°	75.99°	-60.47°	82.99°	127.28°	15.31Å	8.1
4jpw_HL	112.65°	71.66°	-58.66°	89.39°	123.36°	16.92Å	8.1
4ydv_BA	114.33°	72.59°	-62.69°	84.07°	123.51°	16.29Å	8.2

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV26/TRAJ13
Species	human

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	EENLLDFVRF
Antigen Length	10

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*4405

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B2	B3	B4	B5	B6	B7	B8	B9
T	G	V	S	Q	N	P	R
B10	B11	B12	B13	B14	B15	B16	B17
H	K	I	T	K	R	G	Q
B18	B19	B20	B21	B22	B23	B24	B25
N	V	T	F	R	C	D	P
B26	B27	B28	B29	B37	B38	B39	B40
I	S	E	H	N	R	L	Y
B41	B42	B43	B44	B45	B46	B47	B48
W	Y	R	Q	T	L	G	Q
B49	B50	B51	B52	B53	B54	B55	B56
G	P	E	F	L	T	Y	F
B57	B58	B63	B64	B65	B66	B67	B68
Q	N	E	A	Q	L	E	K
B69	B70	B71	B72	B73	B74	B75	B76
S	R	L	L	S	D	R	F
B77	B78	B79	B80	B81	B83	B84	B85
S	A	E	R	P	K	G	S
B86	B87	B88	B89	B90	B91	B92	B93
F	S	T	L	E	I	Q	R
B94	B95	B96	B97	B98	B99	B100	B101
T	E	Q	G	D	S	A	M
B102	B103	B104	B105	B106	B107	B108	B109
Y	L	C	A	S	R	Y	R
B110	B111	B112	B113	B114	B115	B116	B117
D	D	S	Y	N	E	Q	F
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	T
B126	B127
V	L

FASTA file

A2	A3	A4	A5	A6	A8	A9	A10
A	K	T	T	Q	P	T	S
A11	A12	A13	A14	A15	A16	A17	A18
M	D	C	A	E	G	R	A
A19	A20	A21	A22	A23	A24	A25	A26
A	N	L	P	C	N	H	S
A27	A28	A29	A30	A36	A37	A38	A39
T	I	S	G	N	E	Y	V
A40	A41	A42	A43	A44	A45	A46	A47
Y	W	Y	R	Q	I	H	S
A48	A49	A50	A51	A52	A53	A54	A55
Q	G	P	Q	Y	I	I	H
A56	A57	A58	A64	A65	A66	A67	A68
G	L	K	N	N	E	T	N
A74	A75	A76	A77	A78	A79	A80	A81
E	M	A	S	L	I	I	T
A82	A83	A84	A85	A86	A87	A88	A89
E	D	R	K	S	S	T	L
A90	A91	A92	A93	A94	A95	A96	A97
I	L	P	H	A	T	L	R
A98	A99	A100	A101	A102	A103	A104	A105
D	T	A	V	Y	Y	C	I
A106	A107	A108	A109	A113	A114	A115	A116
V	W	G	G	Y	Q	K	V
A117	A118	A119	A120	A121	A122	A123	A124
T	F	G	T	G	T	K	L
A125	A126	A127	A128
Q	V	I	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASRYRDDSYNEQF	None	13
CDRB2	FQNEAQ	None	6
CDRB1	SEHNR	None	5
CDRA3	IVWGGYQKVT	None	10
CDRA2	GLKNN	None	5
CDRA1	TISGNEY	None	7

Orientation and docking angles:

Angle	Value
BC2	112.22°
BC1	71.85°
BA	-61.83°
AC2	88.91°
AC1	130.24°
dc	18.26Å
Docking angle	60.43°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4gg6_FE	111.17°	73.07°	-62.86°	89.77°	131.55°	16.94Å	2.8
4gg6_HG	110.99°	73.29°	-63.02°	90.06°	131.30°	16.97Å	3.0
5d2n_FC	110.14°	72.01°	-59.58°	87.06°	130.65°	17.38Å	3.7
1mi5_ED	109.30°	72.73°	-63.43°	87.70°	131.17°	17.09Å	3.9
6avg_DC	111.12°	74.76°	-63.24°	87.80°	129.13°	17.03Å	4.0

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	7.7
4xvs_HL	115.53°	75.40°	-59.24°	84.30°	126.77°	16.08Å	8.3
4hfu_HL	112.36°	71.78°	-58.26°	83.56°	125.23°	16.51Å	8.3
4lsv_HL	112.42°	71.79°	-57.42°	87.34°	123.18°	16.92Å	8.6
2w65_AB	112.61°	73.10°	-59.37°	85.00°	123.28°	16.61Å	8.6

O / N

TCR Details:

Item	Info
VB chain	O
VA chain	N
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV26/TRAJ13
Species	human

Antigen Details:

Item	Info
Antigen Chain	M
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	EENLLDFVRF
Antigen Length	10

MHC details:

Item	Info
MHC Chain	K \| L
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*4405

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B2	B3	B4	B5	B6	B7	B8	B9
T	G	V	S	Q	N	P	R
B10	B11	B12	B13	B14	B15	B16	B17
H	K	I	T	K	R	G	Q
B18	B19	B20	B21	B22	B23	B24	B25
N	V	T	F	R	C	D	P
B26	B27	B28	B29	B37	B38	B39	B40
I	S	E	H	N	R	L	Y
B41	B42	B43	B44	B45	B46	B47	B48
W	Y	R	Q	T	L	G	Q
B49	B50	B51	B52	B53	B54	B55	B56
G	P	E	F	L	T	Y	F
B57	B58	B63	B64	B65	B66	B67	B68
Q	N	E	A	Q	L	E	K
B69	B70	B71	B72	B73	B74	B75	B76
S	R	L	L	S	D	R	F
B77	B78	B79	B80	B81	B83	B84	B85
S	A	E	R	P	K	G	S
B86	B87	B88	B89	B90	B91	B92	B93
F	S	T	L	E	I	Q	R
B94	B95	B96	B97	B98	B99	B100	B101
T	E	Q	G	D	S	A	M
B102	B103	B104	B105	B106	B107	B108	B109
Y	L	C	A	S	R	Y	R
B110	B111	B112	B113	B114	B115	B116	B117
D	D	S	Y	N	E	Q	F
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	T
B126	B127
V	L

FASTA file

A2	A3	A4	A5	A6	A8	A9	A10
A	K	T	T	Q	P	T	S
A11	A12	A13	A14	A15	A16	A17	A18
M	D	C	A	E	G	R	A
A19	A20	A21	A22	A23	A24	A25	A26
A	N	L	P	C	N	H	S
A27	A28	A29	A30	A36	A37	A38	A39
T	I	S	G	N	E	Y	V
A40	A41	A42	A43	A44	A45	A46	A47
Y	W	Y	R	Q	I	H	S
A48	A49	A50	A51	A52	A53	A54	A55
Q	G	P	Q	Y	I	I	H
A56	A57	A58	A64	A65	A66	A67	A68
G	L	K	N	N	E	T	N
A74	A75	A76	A77	A78	A79	A80	A81
E	M	A	S	L	I	I	T
A82	A83	A84	A85	A86	A87	A88	A89
E	D	R	K	S	S	T	L
A90	A91	A92	A93	A94	A95	A96	A97
I	L	P	H	A	T	L	R
A98	A99	A100	A101	A102	A103	A104	A105
D	T	A	V	Y	Y	C	I
A106	A107	A108	A109	A113	A114	A115	A116
V	W	G	G	Y	Q	K	V
A117	A118	A119	A120	A121	A122	A123	A124
T	F	G	T	G	T	K	L
A125	A126	A127	A128
Q	V	I	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASRYRDDSYNEQF	None	13
CDRB2	FQNEAQ	None	6
CDRB1	SEHNR	None	5
CDRA3	IVWGGYQKVT	None	10
CDRA2	GLKNN	None	5
CDRA1	TISGNEY	None	7

Orientation and docking angles:

Angle	Value
BC2	112.06°
BC1	72.11°
BA	-62.92°
AC2	87.81°
AC1	130.26°
dc	18.12Å
Docking angle	58.23°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4gg6_FE	111.17°	73.07°	-62.86°	89.77°	131.55°	16.94Å	2.9
1kgc_ED	109.35°	71.85°	-63.15°	86.71°	130.57°	17.26Å	3.1
6avg_DC	111.12°	74.76°	-63.24°	87.80°	129.13°	17.03Å	3.2
4gg6_HG	110.99°	73.29°	-63.02°	90.06°	131.30°	16.97Å	3.2
1mi5_ED	109.30°	72.73°	-63.43°	87.70°	131.17°	17.09Å	3.2

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4xvs_HL	115.53°	75.40°	-59.24°	84.30°	126.77°	16.08Å	8.1
4hfu_HL	112.36°	71.78°	-58.26°	83.56°	125.23°	16.51Å	8.2
4ydv_BA	114.33°	72.59°	-62.69°	84.07°	123.51°	16.29Å	8.3
4jpw_HL	112.65°	71.66°	-58.66°	89.39°	123.36°	16.92Å	8.4
4s1q_HL	115.45°	75.99°	-60.47°	82.99°	127.28°	15.31Å	8.5

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