Details for 5e6i

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 TCR Pf8 in complex with Flu Mp(58-66) Epitope Presented By HLA-A2

Item	Info
PDB	5e6i
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	4Å
Number of TCRs	4

Paired chains information

This PDB has 4 TCR(s).

B / A

TCR Details:

Item	Info
VB chain	B
VA chain	A
VB IMGT details	TRBV27/TRBJ2
VA IMGT details	TRAV35/TRAJ37
Species	human

Antigen Details:

Item	Info
Antigen Chain	E
Antigen Type	Peptide
Antigen Organism	INFLUENZA A VIRUS
Antigen Sequence	GILGFVFTL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	C \| D
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-A*0201

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
G	Q	Q	L	N	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	M	F	I	Q	E	G
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	S	M	N	C	T
A25	A26	A27	A28	A29	A37	A38	A39
S	S	S	I	F	N	T	W
A40	A41	A42	A43	A44	A45	A46	A47
L	W	Y	K	Q	E	P	G
A48	A49	A50	A51	A52	A53	A54	A55
E	G	P	V	L	L	I	A
A56	A57	A58	A59	A63	A64	A65	A66
L	Y	K	A	G	E	L	T
A67	A68	A74	A75	A76	A77	A78	A79
S	N	G	R	L	T	A	Q
A80	A81	A82	A83	A84	A85	A86	A87
F	G	I	T	R	K	D	S
A88	A89	A90	A91	A92	A93	A94	A95
F	L	N	I	S	A	S	I
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	V	G	I	Y	F
A104	A105	A106	A107	A108	A109	A110	A111
C	A	G	P	G	G	S	S
A112	A113	A114	A115	A116	A117	A118	A119
N	T	G	K	L	I	F	G
A120	A121	A122	A123	A124	A125	A126	A127
Q	G	T	T	L	Q	V	K
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLIYPGELF	None	11
CDRB2	SMNVEV	None	6
CDRB1	MNHEY	None	5
CDRA3	AGPGGSSNTGKLI	None	13
CDRA2	LYKAGEL	None	7
CDRA1	SIFNT	None	5

Orientation and docking angles:

Angle	Value
BC2	109.82°
BC1	71.78°
BA	-59.43°
AC2	74.78°
AC1	123.96°
dc	16.82Å
Docking angle	63.73°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
3c6l_BA	111.75°	72.89°	-59.46°	75.44°	123.92°	16.61Å	2.3
3c6l_FE	111.86°	72.92°	-59.42°	75.57°	123.91°	16.62Å	2.5
1tcr_BA	108.17°	70.94°	-61.03°	74.90°	121.61°	16.78Å	3.4
1u3h_FE	107.39°	72.28°	-61.98°	75.12°	124.59°	16.64Å	3.6
7na5_ED	107.65°	72.03°	-60.43°	77.41°	125.33°	16.45Å	3.8

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
2vxt_HL	112.53°	71.75°	-60.55°	78.20°	120.37°	16.05Å	5.8
1fbi_QP	113.29°	73.42°	-61.95°	78.25°	123.04°	15.83Å	5.9
5kte_HL	112.24°	69.79°	-60.09°	77.74°	119.92°	16.52Å	6.0
3wih_IM	112.74°	73.69°	-62.39°	76.91°	120.77°	15.54Å	6.1
4osu_HL	113.36°	71.18°	-59.13°	79.75°	123.24°	15.69Å	6.3

H / G

TCR Details:

Item	Info
VB chain	H
VA chain	G
VB IMGT details	TRBV27/TRBJ2
VA IMGT details	TRAV35/TRAJ37
Species	human

Antigen Details:

Item	Info
Antigen Chain	K
Antigen Type	Peptide
Antigen Organism	INFLUENZA A VIRUS
Antigen Sequence	GILGFVFTL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	I \| J
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-A*0201

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
G	Q	Q	L	N	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	M	F	I	Q	E	G
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	S	M	N	C	T
A25	A26	A27	A28	A29	A37	A38	A39
S	S	S	I	F	N	T	W
A40	A41	A42	A43	A44	A45	A46	A47
L	W	Y	K	Q	E	P	G
A48	A49	A50	A51	A52	A53	A54	A55
E	G	P	V	L	L	I	A
A56	A57	A58	A59	A63	A64	A65	A66
L	Y	K	A	G	E	L	T
A67	A68	A74	A75	A76	A77	A78	A79
S	N	G	R	L	T	A	Q
A80	A81	A82	A83	A84	A85	A86	A87
F	G	I	T	R	K	D	S
A88	A89	A90	A91	A92	A93	A94	A95
F	L	N	I	S	A	S	I
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	V	G	I	Y	F
A104	A105	A106	A107	A108	A109	A110	A111
C	A	G	P	G	G	S	S
A112	A113	A114	A115	A116	A117	A118	A119
N	T	G	K	L	I	F	G
A120	A121	A122	A123	A124	A125	A126	A127
Q	G	T	T	L	Q	V	K
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLIYPGELF	None	11
CDRB2	SMNVEV	None	6
CDRB1	MNHEY	None	5
CDRA3	AGPGGSSNTGKLI	None	13
CDRA2	LYKAGEL	None	7
CDRA1	SIFNT	None	5

Orientation and docking angles:

Angle	Value
BC2	109.32°
BC1	70.63°
BA	-61.83°
AC2	71.75°
AC1	124.34°
dc	17.06Å
Docking angle	66.31°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
1d9k_FE	110.68°	72.21°	-62.85°	71.96°	124.87°	16.59Å	2.4
6dfw_HG	107.05°	70.11°	-60.64°	72.85°	125.63°	17.16Å	3.1
1d9k_BA	110.02°	72.46°	-64.28°	73.85°	124.11°	16.70Å	3.8
4p46_BA	108.81°	71.44°	-65.09°	73.62°	124.48°	16.80Å	3.9
1u3h_BA	109.33°	71.68°	-64.54°	73.89°	122.91°	16.82Å	3.9

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	5.4
3wih_IM	112.74°	73.69°	-62.39°	76.91°	120.77°	15.54Å	7.9
1jv5_BA	111.45°	73.74°	-67.77°	74.39°	122.07°	15.49Å	8.0
4uim_AB	109.49°	71.42°	-65.63°	76.99°	119.77°	15.95Å	8.0
4x4x_CD	112.33°	72.96°	-60.80°	78.66°	125.88°	15.67Å	8.2

L / F

TCR Details:

Item	Info
VB chain	L
VA chain	F
VB IMGT details	TRBV27/TRBJ2
VA IMGT details	TRAV35/TRAJ37
Species	human

Antigen Details:

Item	Info
Antigen Chain	O
Antigen Type	Peptide
Antigen Organism	INFLUENZA A VIRUS
Antigen Sequence	GILGFVFTL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	M \| N
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-A*0201

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
G	Q	Q	L	N	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	M	F	I	Q	E	G
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	S	M	N	C	T
A25	A26	A27	A28	A29	A37	A38	A39
S	S	S	I	F	N	T	W
A40	A41	A42	A43	A44	A45	A46	A47
L	W	Y	K	Q	E	P	G
A48	A49	A50	A51	A52	A53	A54	A55
E	G	P	V	L	L	I	A
A56	A57	A58	A59	A63	A64	A65	A66
L	Y	K	A	G	E	L	T
A67	A68	A74	A75	A76	A77	A78	A79
S	N	G	R	L	T	A	Q
A80	A81	A82	A83	A84	A85	A86	A87
F	G	I	T	R	K	D	S
A88	A89	A90	A91	A92	A93	A94	A95
F	L	N	I	S	A	S	I
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	V	G	I	Y	F
A104	A105	A106	A107	A108	A109	A110	A111
C	A	G	P	G	G	S	S
A112	A113	A114	A115	A116	A117	A118	A119
N	T	G	K	L	I	F	G
A120	A121	A122	A123	A124	A125	A126	A127
Q	G	T	T	L	Q	V	K
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLIYPGELF	None	11
CDRB2	SMNVEV	None	6
CDRB1	MNHEY	None	5
CDRA3	AGPGGSSNTGKLI	None	13
CDRA2	LYKAGEL	None	7
CDRA1	SIFNT	None	5

Orientation and docking angles:

Angle	Value
BC2	110.43°
BC1	71.17°
BA	-60.84°
AC2	72.67°
AC1	125.00°
dc	17.08Å
Docking angle	63.11°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
1d9k_FE	110.68°	72.21°	-62.85°	71.96°	124.87°	16.59Å	2.4
6dfw_HG	107.05°	70.11°	-60.64°	72.85°	125.63°	17.16Å	3.6
3c6l_BA	111.75°	72.89°	-59.46°	75.44°	123.92°	16.61Å	4.0
1d9k_BA	110.02°	72.46°	-64.28°	73.85°	124.11°	16.70Å	4.0
3c6l_FE	111.86°	72.92°	-59.42°	75.57°	123.91°	16.62Å	4.1

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	6.7
4x4x_CD	112.33°	72.96°	-60.80°	78.66°	125.88°	15.67Å	6.7
1fbi_QP	113.29°	73.42°	-61.95°	78.25°	123.04°	15.83Å	7.1
3wih_IM	112.74°	73.69°	-62.39°	76.91°	120.77°	15.54Å	7.2
1dvf_DC	114.14°	72.16°	-63.08°	77.80°	122.38°	15.86Å	7.4

Q / P

TCR Details:

Item	Info
VB chain	Q
VA chain	P
VB IMGT details	TRBV27/TRBJ2
VA IMGT details	TRAV35/TRAJ37
Species	human

Antigen Details:

Item	Info
Antigen Chain	T
Antigen Type	Peptide
Antigen Organism	INFLUENZA A VIRUS
Antigen Sequence	GILGFVFTL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	R \| U
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-A*0201

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
G	Q	Q	L	N	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	M	F	I	Q	E	G
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	S	M	N	C	T
A25	A26	A27	A28	A29	A37	A38	A39
S	S	S	I	F	N	T	W
A40	A41	A42	A43	A44	A45	A46	A47
L	W	Y	K	Q	E	P	G
A48	A49	A50	A51	A52	A53	A54	A55
E	G	P	V	L	L	I	A
A56	A57	A58	A59	A63	A64	A65	A66
L	Y	K	A	G	E	L	T
A67	A68	A74	A75	A76	A77	A78	A79
S	N	G	R	L	T	A	Q
A80	A81	A82	A83	A84	A85	A86	A87
F	G	I	T	R	K	D	S
A88	A89	A90	A91	A92	A93	A94	A95
F	L	N	I	S	A	S	I
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	V	G	I	Y	F
A104	A105	A106	A107	A108	A109	A110	A111
C	A	G	P	G	G	S	S
A112	A113	A114	A115	A116	A117	A118	A119
N	T	G	K	L	I	F	G
A120	A121	A122	A123	A124	A125	A126	A127
Q	G	T	T	L	Q	V	K
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLIYPGELF	None	11
CDRB2	SMNVEV	None	6
CDRB1	MNHEY	None	5
CDRA3	AGPGGSSNTGKLI	None	13
CDRA2	LYKAGEL	None	7
CDRA1	SIFNT	None	5

Orientation and docking angles:

Angle	Value
BC2	109.25°
BC1	70.24°
BA	-60.47°
AC2	72.87°
AC1	123.00°
dc	17.20Å
Docking angle	66.28°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
1tcr_BA	108.17°	70.94°	-61.03°	74.90°	121.61°	16.78Å	2.9
6dfw_HG	107.05°	70.11°	-60.64°	72.85°	125.63°	17.16Å	3.4
1d9k_FE	110.68°	72.21°	-62.85°	71.96°	124.87°	16.59Å	4.0
3c60_BA	107.87°	72.85°	-62.87°	74.17°	122.49°	16.41Å	4.1
3c60_FE	107.89°	72.90°	-62.78°	74.22°	122.48°	16.41Å	4.1

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	5.4
5kte_HL	112.24°	69.79°	-60.09°	77.74°	119.92°	16.52Å	6.6
2vxt_HL	112.53°	71.75°	-60.55°	78.20°	120.37°	16.05Å	7.0
3wih_IM	112.74°	73.69°	-62.39°	76.91°	120.77°	15.54Å	7.2
2vxu_IM	110.96°	71.68°	-62.78°	78.60°	119.89°	16.17Å	7.3

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