Details for 7t2d

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Structure information

Crystal Structure of the B1 TCR in complex with HLA-Dp4-Ply

Item	Info
PDB	7t2d
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	3.4Å
Number of TCRs	4

Paired chains information

This PDB has 4 TCR(s).

E / D

TCR Details:

Item	Info
VB chain	E
VA chain	D
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV19/TRAJ22
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	STREPTOCOCCUS PNEUMONIAE
Antigen Sequence	GATGLAWEWWRTVYE
Antigen Length	15

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH2
MHC Species	human
MHC IMGT details	HLA-DPA10103 / HLA-DPB10401

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
G	A	G	V	S	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
S	N	K	V	T	E	K	G
B17	B18	B19	B20	B21	B22	B23	B24
K	Y	V	E	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	T	A	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	S	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	P	E	F	L	I	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	Q	G	T	G	A	A	D
B68	B69	B70	B71	B72	B73	B74	B75
D	S	G	L	P	N	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	F	A	V	R	P	E	G
B85	B86	B87	B88	B89	B90	B91	B92
S	V	S	T	L	K	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	E	R	G	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
V	Y	L	C	A	S	S	H
B109	B110	B113	B114	B115	B116	B117	B118
R	E	G	E	T	Q	Y	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	L	V
B127
L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
A	Q	K	V	T	Q	A	Q
A9	A10	A11	A12	A13	A14	A15	A16
T	E	I	S	V	V	E	K
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	T	L	D	C	V
A25	A26	A27	A28	A29	A30	A36	A37
Y	E	T	R	D	T	T	Y
A38	A39	A40	A41	A42	A43	A44	A45
Y	L	F	W	Y	K	Q	P
A46	A47	A48	A49	A50	A51	A52	A53
P	S	G	E	L	V	F	L
A54	A55	A56	A57	A58	A59	A62	A63
I	R	R	N	S	F	D	E
A64	A65	A66	A67	A68	A74	A75	A76
Q	N	E	I	S	G	R	Y
A77	A78	A79	A80	A81	A82	A83	A84
S	W	N	F	Q	K	S	T
A85	A86	A87	A88	A89	A90	A91	A92
S	S	F	N	F	T	I	T
A93	A94	A95	A96	A97	A98	A99	A100
A	S	Q	V	V	D	S	A
A101	A102	A103	A104	A105	A106	A107	A108
V	Y	F	C	A	L	S	G
A109	A113	A114	A115	A116	A117	A118	A119
S	A	R	Q	L	T	F	G
A120	A121	A122	A123	A124	A125	A126	A127
S	G	T	Q	L	T	V	L
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSHREGETQY	None	11
CDRB2	FQGTGA	None	6
CDRB1	SGHTA	None	5
CDRA3	ALSGSARQLT	None	10
CDRA2	RNSFDEQN	None	8
CDRA1	TRDTTYY	None	7

Orientation and docking angles:

Angle	Value
BC2	102.83°
BC1	73.36°
BA	-58.93°
AC2	80.80°
AC1	122.46°
dc	16.08Å
Docking angle	54.14°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4e41_ED	102.89°	73.20°	-60.14°	80.58°	122.38°	15.80Å	1.3
3vxq_BA	102.71°	73.42°	-58.65°	80.10°	120.88°	15.91Å	1.8
4pjx_FE	103.82°	72.61°	-59.27°	80.63°	124.00°	16.56Å	2.1
6pug_ED	103.58°	72.88°	-60.35°	80.20°	123.58°	16.68Å	2.2
5ks9_HG	103.96°	73.13°	-60.30°	79.64°	123.33°	15.94Å	2.3

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	7.4
4hxb_HL	109.66°	72.24°	-59.19°	82.14°	119.35°	16.41Å	7.7
3mo1_BA	109.77°	73.00°	-58.46°	81.03°	119.12°	16.26Å	7.7
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	7.7
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	7.8

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV19/TRAJ22
Species	human

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	STREPTOCOCCUS PNEUMONIAE
Antigen Sequence	GATGLAWEWWRTVYE
Antigen Length	15

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	MH2
MHC Species	human
MHC IMGT details	HLA-DPA10103 / HLA-DPB10401

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
G	A	G	V	S	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
S	N	K	V	T	E	K	G
B17	B18	B19	B20	B21	B22	B23	B24
K	Y	V	E	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	T	A	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	S	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	P	E	F	L	I	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	Q	G	T	G	A	A	D
B68	B69	B70	B71	B72	B73	B74	B75
D	S	G	L	P	N	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	F	A	V	R	P	E	G
B85	B86	B87	B88	B89	B90	B91	B92
S	V	S	T	L	K	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	E	R	G	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
V	Y	L	C	A	S	S	H
B109	B110	B113	B114	B115	B116	B117	B118
R	E	G	E	T	Q	Y	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	L	V
B127
L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
A	Q	K	V	T	Q	A	Q
A9	A10	A11	A12	A13	A14	A15	A16
T	E	I	S	V	V	E	K
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	T	L	D	C	V
A25	A26	A27	A28	A29	A30	A36	A37
Y	E	T	R	D	T	T	Y
A38	A39	A40	A41	A42	A43	A44	A45
Y	L	F	W	Y	K	Q	P
A46	A47	A48	A49	A50	A51	A52	A53
P	S	G	E	L	V	F	L
A54	A55	A56	A57	A58	A59	A62	A63
I	R	R	N	S	F	D	E
A64	A65	A66	A67	A68	A74	A75	A76
Q	N	E	I	S	G	R	Y
A77	A78	A79	A80	A81	A82	A83	A84
S	W	N	F	Q	K	S	T
A85	A86	A87	A88	A89	A90	A91	A92
S	S	F	N	F	T	I	T
A93	A94	A95	A96	A97	A98	A99	A100
A	S	Q	V	V	D	S	A
A101	A102	A103	A104	A105	A106	A107	A108
V	Y	F	C	A	L	S	G
A109	A113	A114	A115	A116	A117	A118	A119
S	A	R	Q	L	T	F	G
A120	A121	A122	A123	A124	A125	A126	A127
S	G	T	Q	L	T	V	L
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSHREGETQY	None	11
CDRB2	FQGTGA	None	6
CDRB1	SGHTA	None	5
CDRA3	ALSGSARQLT	None	10
CDRA2	RNSFDEQN	None	8
CDRA1	TRDTTYY	None	7

Orientation and docking angles:

Angle	Value
BC2	98.51°
BC1	72.33°
BA	-62.82°
AC2	78.01°
AC1	120.61°
dc	15.98Å
Docking angle	55.41°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4p2o_DC	97.65°	73.22°	-63.70°	79.93°	120.65°	15.65Å	2.5
6bga_DC	97.05°	72.68°	-63.59°	79.78°	120.33°	15.68Å	2.5
4may_DC	101.00°	72.85°	-63.47°	77.70°	121.21°	15.54Å	2.7
4grl_DC	101.09°	72.67°	-62.95°	78.25°	121.42°	15.62Å	2.8
3pl6_DC	101.57°	73.02°	-63.19°	78.32°	121.38°	15.56Å	3.3

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	9.7
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	9.8

O / N

TCR Details:

Item	Info
VB chain	O
VA chain	N
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV19/TRAJ22
Species	human

Antigen Details:

Item	Info
Antigen Chain	M
Antigen Type	Peptide
Antigen Organism	STREPTOCOCCUS PNEUMONIAE
Antigen Sequence	GATGLAWEWWRTVYE
Antigen Length	15

MHC details:

Item	Info
MHC Chain	K \| L
MHC Type	MH2
MHC Species	human
MHC IMGT details	HLA-DPA10103 / HLA-DPB10401

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
G	A	G	V	S	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
S	N	K	V	T	E	K	G
B17	B18	B19	B20	B21	B22	B23	B24
K	Y	V	E	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	T	A	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	S	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	P	E	F	L	I	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	Q	G	T	G	A	A	D
B68	B69	B70	B71	B72	B73	B74	B75
D	S	G	L	P	N	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	F	A	V	R	P	E	G
B85	B86	B87	B88	B89	B90	B91	B92
S	V	S	T	L	K	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	E	R	G	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
V	Y	L	C	A	S	S	H
B109	B110	B113	B114	B115	B116	B117	B118
R	E	G	E	T	Q	Y	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	L	V
B127
L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
A	Q	K	V	T	Q	A	Q
A9	A10	A11	A12	A13	A14	A15	A16
T	E	I	S	V	V	E	K
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	T	L	D	C	V
A25	A26	A27	A28	A29	A30	A36	A37
Y	E	T	R	D	T	T	Y
A38	A39	A40	A41	A42	A43	A44	A45
Y	L	F	W	Y	K	Q	P
A46	A47	A48	A49	A50	A51	A52	A53
P	S	G	E	L	V	F	L
A54	A55	A56	A57	A58	A59	A62	A63
I	R	R	N	S	F	D	E
A64	A65	A66	A67	A68	A74	A75	A76
Q	N	E	I	S	G	R	Y
A77	A78	A79	A80	A81	A82	A83	A84
S	W	N	F	Q	K	S	T
A85	A86	A87	A88	A89	A90	A91	A92
S	S	F	N	F	T	I	T
A93	A94	A95	A96	A97	A98	A99	A100
A	S	Q	V	V	D	S	A
A101	A102	A103	A104	A105	A106	A107	A108
V	Y	F	C	A	L	S	G
A109	A113	A114	A115	A116	A117	A118	A119
S	A	R	Q	L	T	F	G
A120	A121	A122	A123	A124	A125	A126	A127
S	G	T	Q	L	T	V	L
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSHREGETQY	None	11
CDRB2	FQGTGA	None	6
CDRB1	SGHTA	None	5
CDRA3	ALSGSARQLT	None	10
CDRA2	RNSFDEQN	None	8
CDRA1	TRDTTYY	None	7

Orientation and docking angles:

Angle	Value
BC2	98.58°
BC1	72.77°
BA	-62.78°
AC2	79.21°
AC1	121.28°
dc	15.79Å
Docking angle	58.20°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4p2o_DC	97.65°	73.22°	-63.70°	79.93°	120.65°	15.65Å	1.7
6bga_DC	97.05°	72.68°	-63.59°	79.78°	120.33°	15.68Å	2.1
4grl_DC	101.09°	72.67°	-62.95°	78.25°	121.42°	15.62Å	2.7
4may_DC	101.00°	72.85°	-63.47°	77.70°	121.21°	15.54Å	2.9
3qjf_DC	97.53°	73.90°	-60.55°	80.10°	120.92°	15.55Å	2.9

T / S

TCR Details:

Item	Info
VB chain	T
VA chain	S
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV19/TRAJ22
Species	human

Antigen Details:

Item	Info
Antigen Chain	R
Antigen Type	Peptide
Antigen Organism	STREPTOCOCCUS PNEUMONIAE
Antigen Sequence	GATGLAWEWWRTVYE
Antigen Length	15

MHC details:

Item	Info
MHC Chain	P \| Q
MHC Type	MH2
MHC Species	human
MHC IMGT details	HLA-DPA10103 / HLA-DPB10401

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
G	A	G	V	S	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
S	N	K	V	T	E	K	G
B17	B18	B19	B20	B21	B22	B23	B24
K	Y	V	E	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	T	A	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	S	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	P	E	F	L	I	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	Q	G	T	G	A	A	D
B68	B69	B70	B71	B72	B73	B74	B75
D	S	G	L	P	N	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	F	A	V	R	P	E	G
B85	B86	B87	B88	B89	B90	B91	B92
S	V	S	T	L	K	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	E	R	G	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
V	Y	L	C	A	S	S	H
B109	B110	B113	B114	B115	B116	B117	B118
R	E	G	E	T	Q	Y	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	L	V
B127
L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
A	Q	K	V	T	Q	A	Q
A9	A10	A11	A12	A13	A14	A15	A16
T	E	I	S	V	V	E	K
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	T	L	D	C	V
A25	A26	A27	A28	A29	A30	A36	A37
Y	E	T	R	D	T	T	Y
A38	A39	A40	A41	A42	A43	A44	A45
Y	L	F	W	Y	K	Q	P
A46	A47	A48	A49	A50	A51	A52	A53
P	S	G	E	L	V	F	L
A54	A55	A56	A57	A58	A59	A62	A63
I	R	R	N	S	F	D	E
A64	A65	A66	A67	A68	A74	A75	A76
Q	N	E	I	S	G	R	Y
A77	A78	A79	A80	A81	A82	A83	A84
S	W	N	F	Q	K	S	T
A85	A86	A87	A88	A89	A90	A91	A92
S	S	F	N	F	T	I	T
A93	A94	A95	A96	A97	A98	A99	A100
A	S	Q	V	V	D	S	A
A101	A102	A103	A104	A105	A106	A107	A108
V	Y	F	C	A	L	S	G
A109	A113	A114	A115	A116	A117	A118	A119
S	A	R	Q	L	T	F	G
A120	A121	A122	A123	A124	A125	A126	A127
S	G	T	Q	L	T	V	L
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSHREGETQY	None	11
CDRB2	FQGTGA	None	6
CDRB1	SGHTA	None	5
CDRA3	ALSGSARQLT	None	10
CDRA2	RNSFDEQN	None	8
CDRA1	TRDTTYY	None	7

Orientation and docking angles:

Angle	Value
BC2	98.57°
BC1	72.81°
BA	-63.12°
AC2	78.80°
AC1	121.48°
dc	15.70Å
Docking angle	55.49°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4p2o_DC	97.65°	73.22°	-63.70°	79.93°	120.65°	15.65Å	1.8
6bga_DC	97.05°	72.68°	-63.59°	79.78°	120.33°	15.68Å	2.2
4grl_DC	101.09°	72.67°	-62.95°	78.25°	121.42°	15.62Å	2.6
4may_DC	101.00°	72.85°	-63.47°	77.70°	121.21°	15.54Å	2.7
3pl6_DC	101.57°	73.02°	-63.19°	78.32°	121.38°	15.56Å	3.1

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	10.0

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