Details for 5swz

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Structure information

Crystal Structure of Np1-B17 TCR-H2Db-Np complex

Item	Info
PDB	5swz
Organism	MUS MUSCULUS
Method	X-RAY DIFFRACTION
Resolution	2.65Å
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	TRBV17/TRBJ2
VA IMGT details	TRAV14/TRAJ15
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	UNIDENTIFIED INFLUENZA VIRUS
Antigen Sequence	ASNENMETM
Antigen Length	9

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	mouse
MHC IMGT details	H2-D1b

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

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	Q	Q	V	R	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	L	T	V	W	E	G
A17	A18	A19	A20	A21	A22	A23	A24
E	T	A	I	L	N	C	S
A25	A26	A27	A28	A29	A36	A37	A38
Y	E	D	S	T	F	N	Y
A39	A40	A41	A42	A43	A44	A45	A46
F	P	W	Y	Q	Q	F	P
A47	A48	A49	A50	A51	A52	A53	A54
G	E	G	P	A	L	L	I
A55	A56	A57	A58	A59	A63	A64	A65
S	I	R	S	V	S	D	K
A66	A67	A68	A74	A75	A76	A77	A78
K	E	D	G	R	F	T	I
A79	A80	A81	A82	A83	A84	A85	A86
F	F	N	K	R	E	K	K
A87	A88	A89	A90	A91	A92	A93	A94
L	S	L	H	I	T	D	S
A95	A96	A97	A98	A99	A100	A101	A102
Q	P	G	D	S	A	T	Y
A103	A104	A105	A106	A107	A108	A109	A110
F	C	A	A	S	E	T	S
A112	A113	A114	A115	A116	A117	A118	A119
G	S	W	Q	L	I	F	G
A120	A121	A122	A123	A124	A125	A126	A127
S	G	T	T	V	S	V	S
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSRDLGRDTQY	None	12
CDRB2	YYDKIL	None	6
CDRB1	MNHDT	None	5
CDRA3	AASETSGSWQLI	None	12
CDRA2	IRSVSDK	None	7
CDRA1	DSTFNY	None	6

Orientation and docking angles:

Angle	Value
BC2	102.97°
BC1	72.96°
BA	-69.53°
AC2	75.98°
AC1	122.86°
dc	16.87Å
Docking angle	52.08°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2cdg_BA	101.93°	71.70°	-70.24°	76.68°	122.64°	16.70Å	1.9
5d7l_ED	101.37°	72.18°	-70.30°	75.68°	121.34°	16.81Å	2.5
7jwi_ED	102.83°	72.70°	-70.72°	73.61°	121.98°	16.76Å	2.8
6cqn_ED	103.61°	72.65°	-67.65°	75.37°	120.90°	16.00Å	3.0
6pvc_HG	103.78°	74.08°	-67.41°	78.04°	123.24°	16.39Å	3.3

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	5.4
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	5.9
12e8_HL	106.48°	69.23°	-70.96°	74.63°	118.60°	16.05Å	7.0
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	7.3
4uim_CD	109.21°	71.18°	-68.12°	75.36°	117.53°	16.19Å	8.6

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV17/TRBJ2
VA IMGT details	TRAV14/TRAJ15
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	UNIDENTIFIED INFLUENZA VIRUS
Antigen Sequence	ASNENMETM
Antigen Length	9

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	MH1
MHC Species	mouse
MHC IMGT details	H2-D1b

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

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	Q	Q	V	R	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	L	T	V	W	E	G
A17	A18	A19	A20	A21	A22	A23	A24
E	T	A	I	L	N	C	S
A25	A26	A27	A28	A29	A36	A37	A38
Y	E	D	S	T	F	N	Y
A39	A40	A41	A42	A43	A44	A45	A46
F	P	W	Y	Q	Q	F	P
A47	A48	A49	A50	A51	A52	A53	A54
G	E	G	P	A	L	L	I
A55	A56	A57	A58	A59	A63	A64	A65
S	I	R	S	V	S	D	K
A66	A67	A68	A74	A75	A76	A77	A78
K	E	D	G	R	F	T	I
A79	A80	A81	A82	A83	A84	A85	A86
F	F	N	K	R	E	K	K
A87	A88	A89	A90	A91	A92	A93	A94
L	S	L	H	I	T	D	S
A95	A96	A97	A98	A99	A100	A101	A102
Q	P	G	D	S	A	T	Y
A103	A104	A105	A106	A107	A108	A109	A110
F	C	A	A	S	E	T	S
A112	A113	A114	A115	A116	A117	A118	A119
G	S	W	Q	L	I	F	G
A120	A121	A122	A123	A124	A125	A126	A127
S	G	T	T	V	S	V	S
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSRDLGRDTQY	None	12
CDRB2	YYDKIL	None	6
CDRB1	MNHDT	None	5
CDRA3	AASETSGSWQLI	None	12
CDRA2	IRSVSDK	None	7
CDRA1	DSTFNY	None	6

Orientation and docking angles:

Angle	Value
BC2	101.31°
BC1	73.66°
BA	-71.00°
AC2	74.12°
AC1	121.61°
dc	16.68Å
Docking angle	52.28°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
7jwi_ED	102.83°	72.70°	-70.72°	73.61°	121.98°	16.76Å	1.9
5d7l_HG	100.58°	73.05°	-69.45°	73.19°	120.48°	16.93Å	2.3
5d7l_ED	101.37°	72.18°	-70.30°	75.68°	121.34°	16.81Å	2.3
2cdg_BA	101.93°	71.70°	-70.24°	76.68°	122.64°	16.70Å	3.5
6cqr_ED	102.63°	72.40°	-68.09°	74.17°	120.23°	15.99Å	3.8

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	6.1
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	7.1
12e8_HL	106.48°	69.23°	-70.96°	74.63°	118.60°	16.05Å	7.5
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	9.0
4uim_CD	109.21°	71.18°	-68.12°	75.36°	117.53°	16.19Å	9.8

O / N

TCR Details:

Item	Info
VB chain	O
VA chain	N
VB IMGT details	TRBV17/TRBJ2
VA IMGT details	TRAV14/TRAJ15
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	M
Antigen Type	Peptide
Antigen Organism	UNIDENTIFIED INFLUENZA VIRUS
Antigen Sequence	ASNENMETM
Antigen Length	9

MHC details:

Item	Info
MHC Chain	K \| L
MHC Type	MH1
MHC Species	mouse
MHC IMGT details	H2-D1b

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

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	Q	Q	V	R	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	L	T	V	W	E	G
A17	A18	A19	A20	A21	A22	A23	A24
E	T	A	I	L	N	C	S
A25	A26	A27	A28	A29	A36	A37	A38
Y	E	D	S	T	F	N	Y
A39	A40	A41	A42	A43	A44	A45	A46
F	P	W	Y	Q	Q	F	P
A47	A48	A49	A50	A51	A52	A53	A54
G	E	G	P	A	L	L	I
A55	A56	A57	A58	A59	A63	A64	A65
S	I	R	S	V	S	D	K
A66	A67	A68	A74	A75	A76	A77	A78
K	E	D	G	R	F	T	I
A79	A80	A81	A82	A83	A84	A85	A86
F	F	N	K	R	E	K	K
A87	A88	A89	A90	A91	A92	A93	A94
L	S	L	H	I	T	D	S
A95	A96	A97	A98	A99	A100	A101	A102
Q	P	G	D	S	A	T	Y
A103	A104	A105	A106	A107	A108	A109	A110
F	C	A	A	S	E	T	S
A112	A113	A114	A115	A116	A117	A118	A119
G	S	W	Q	L	I	F	G
A120	A121	A122	A123	A124	A125	A126	A127
S	G	T	T	V	S	V	S
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSRDLGRDTQY	None	12
CDRB2	YYDKIL	None	6
CDRB1	MNHDT	None	5
CDRA3	AASETSGSWQLI	None	12
CDRA2	IRSVSDK	None	7
CDRA1	DSTFNY	None	6

Orientation and docking angles:

Angle	Value
BC2	102.92°
BC1	72.97°
BA	-69.95°
AC2	76.37°
AC1	122.18°
dc	16.87Å
Docking angle	54.19°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2cdg_BA	101.93°	71.70°	-70.24°	76.68°	122.64°	16.70Å	1.7
5d7l_ED	101.37°	72.18°	-70.30°	75.68°	121.34°	16.81Å	2.1
7jwi_ED	102.83°	72.70°	-70.72°	73.61°	121.98°	16.76Å	2.9
6cqn_ED	103.61°	72.65°	-67.65°	75.37°	120.90°	16.00Å	3.0
6pvc_HG	103.78°	74.08°	-67.41°	78.04°	123.24°	16.39Å	3.5

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	5.1
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	6.0
12e8_HL	106.48°	69.23°	-70.96°	74.63°	118.60°	16.05Å	6.6
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	7.7
4uim_CD	109.21°	71.18°	-68.12°	75.36°	117.53°	16.19Å	8.3

T / S

TCR Details:

Item	Info
VB chain	T
VA chain	S
VB IMGT details	TRBV17/TRBJ2
VA IMGT details	TRAV14/TRAJ15
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	R
Antigen Type	Peptide
Antigen Organism	UNIDENTIFIED INFLUENZA VIRUS
Antigen Sequence	ASNENMETM
Antigen Length	9

MHC details:

Item	Info
MHC Chain	P \| Q
MHC Type	MH1
MHC Species	mouse
MHC IMGT details	H2-D1b

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

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	Q	Q	V	R	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	L	T	V	W	E	G
A17	A18	A19	A20	A21	A22	A23	A24
E	T	A	I	L	N	C	S
A25	A26	A27	A28	A29	A36	A37	A38
Y	E	D	S	T	F	N	Y
A39	A40	A41	A42	A43	A44	A45	A46
F	P	W	Y	Q	Q	F	P
A47	A48	A49	A50	A51	A52	A53	A54
G	E	G	P	A	L	L	I
A55	A56	A57	A58	A59	A63	A64	A65
S	I	R	S	V	S	D	K
A66	A67	A68	A74	A75	A76	A77	A78
K	E	D	G	R	F	T	I
A79	A80	A81	A82	A83	A84	A85	A86
F	F	N	K	R	E	K	K
A87	A88	A89	A90	A91	A92	A93	A94
L	S	L	H	I	T	D	S
A95	A96	A97	A98	A99	A100	A101	A102
Q	P	G	D	S	A	T	Y
A103	A104	A105	A106	A107	A108	A109	A110
F	C	A	A	S	E	T	S
A112	A113	A114	A115	A116	A117	A118	A119
G	S	W	Q	L	I	F	G
A120	A121	A122	A123	A124	A125	A126	A127
S	G	T	T	V	S	V	S
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSRDLGRDTQY	None	12
CDRB2	YYDKIL	None	6
CDRB1	MNHDT	None	5
CDRA3	AASETSGSWQLI	None	12
CDRA2	IRSVSDK	None	7
CDRA1	DSTFNY	None	6

Orientation and docking angles:

Angle	Value
BC2	102.55°
BC1	72.71°
BA	-73.06°
AC2	73.13°
AC1	121.22°
dc	16.92Å
Docking angle	53.13°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
7jwi_ED	102.83°	72.70°	-70.72°	73.61°	121.98°	16.76Å	2.5
5d7l_ED	101.37°	72.18°	-70.30°	75.68°	121.34°	16.81Å	4.0
5d7l_HG	100.58°	73.05°	-69.45°	73.19°	120.48°	16.93Å	4.2
8trq_ED	104.82°	72.23°	-72.24°	70.19°	123.22°	17.20Å	4.3
6cqr_JI	103.77°	72.60°	-69.24°	73.97°	118.89°	16.17Å	4.8

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	5.6
12e8_HL	106.48°	69.23°	-70.96°	74.63°	118.60°	16.05Å	6.5
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	7.5
4uin_HL	107.61°	70.78°	-70.27°	77.14°	115.22°	16.35Å	9.5
4uim_CD	109.21°	71.18°	-68.12°	75.36°	117.53°	16.19Å	9.5

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Item	Link
IMGT-numbered structure	Link
Non-annotated structure from the PDB	Link
Summary file for this TCR	Link
Link in the PDB	Link