Details for 5w1v

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Structure information

Structure of the HLA-E-Vmaprtlil/Gf4 TCR complex

Item	Info
PDB	5w1v
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	3.31Å
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	TRBV9/TRBJ1
VA IMGT details	TRAV35/TRAJ53
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	HUMAN HERPESVIRUS 5 STRAIN AD169
Antigen Sequence	VMAPRTLIL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-E*0101

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	S	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	H	L	I	T	A	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	R	V	T	L	R	C	S
B25	B26	B27	B28	B29	B37	B38	B39
P	R	S	G	D	L	S	V
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	Q	Q	S	L	D
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	L	Q	F	L	I	Q
B56	B57	B58	B63	B64	B65	B66	B67
Y	Y	N	G	E	E	R	A
B68	B69	B70	B71	B72	B74	B75	B76
K	G	N	I	L	E	R	F
B77	B78	B79	B80	B81	B83	B84	B85
S	A	Q	Q	F	P	D	L
B86	B87	B88	B89	B90	B91	B92	B93
H	S	E	L	N	L	S	S
B94	B95	B96	B97	B98	B99	B100	B101
L	E	L	G	D	S	A	L
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	A	N
B110	B111	B111A	B112A	B112	B113	B114	B115
P	G	D	S	S	N	E	K
B116	B117	B118	B119	B120	B121	B122	B123
L	F	F	G	S	G	T	Q
B124	B125	B126	B127
L	S	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	D	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	Q	P	L	G	G
A112	A113	A114	A115	A116	A117	A118	A119
S	N	Y	K	L	T	F	G
A120	A121	A122	A123	A124	A125	A126	A127
K	G	T	L	L	T	V	N
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSANPGDSSNEKLF	None	15
CDRB2	YYNGEE	None	6
CDRB1	SGDLS	None	5
CDRA3	AGQPLGGSNYKLT	None	13
CDRA2	LYKAGEL	None	7
CDRA1	SIFNT	None	5

Orientation and docking angles:

Angle	Value
BC2	105.20°
BC1	72.49°
BA	-55.24°
AC2	79.52°
AC1	127.72°
dc	16.57Å
Docking angle	69.34°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5w1w_ED	105.81°	71.13°	-54.40°	77.86°	128.93°	16.65Å	2.7
5yxu_GF	103.74°	70.63°	-55.17°	80.81°	126.54°	16.23Å	3.0
7pbe_JI	106.09°	72.32°	-55.89°	79.51°	124.71°	16.52Å	3.2
6py2_ED	106.09°	73.09°	-52.34°	79.71°	126.93°	16.77Å	3.2
5w1w_TS	105.55°	70.76°	-53.88°	77.65°	129.17°	16.68Å	3.3

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	6.8
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	7.1
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	7.6
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	7.6
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	7.7

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV9/TRBJ1
VA IMGT details	TRAV35/TRAJ53
Species	human

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	HUMAN HERPESVIRUS 5 STRAIN AD169
Antigen Sequence	VMAPRTLIL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-E*0101

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	S	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	H	L	I	T	A	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	R	V	T	L	R	C	S
B25	B26	B27	B28	B29	B37	B38	B39
P	R	S	G	D	L	S	V
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	Q	Q	S	L	D
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	L	Q	F	L	I	Q
B56	B57	B58	B63	B64	B65	B66	B67
Y	Y	N	G	E	E	R	A
B68	B69	B70	B71	B72	B74	B75	B76
K	G	N	I	L	E	R	F
B77	B78	B79	B80	B81	B83	B84	B85
S	A	Q	Q	F	P	D	L
B86	B87	B88	B89	B90	B91	B92	B93
H	S	E	L	N	L	S	S
B94	B95	B96	B97	B98	B99	B100	B101
L	E	L	G	D	S	A	L
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	A	N
B110	B111	B111A	B112A	B112	B113	B114	B115
P	G	D	S	S	N	E	K
B116	B117	B118	B119	B120	B121	B122	B123
L	F	F	G	S	G	T	Q
B124	B125	B126	B127
L	S	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	D	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	Q	P	L	G	G
A112	A113	A114	A115	A116	A117	A118	A119
S	N	Y	K	L	T	F	G
A120	A121	A122	A123	A124	A125	A126	A127
K	G	T	L	L	T	V	N
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSANPGDSSNEKLF	None	15
CDRB2	YYNGEE	None	6
CDRB1	SGDLS	None	5
CDRA3	AGQPLGGSNYKLT	None	13
CDRA2	LYKAGEL	None	7
CDRA1	SIFNT	None	5

Orientation and docking angles:

Angle	Value
BC2	106.34°
BC1	71.84°
BA	-54.74°
AC2	77.38°
AC1	128.22°
dc	16.81Å
Docking angle	69.08°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5w1w_JI	106.10°	70.74°	-54.96°	77.08°	128.55°	16.78Å	1.2
5w1w_ED	105.81°	71.13°	-54.40°	77.86°	128.93°	16.65Å	1.3
5w1w_TS	105.55°	70.76°	-53.88°	77.65°	129.17°	16.68Å	1.9
7rdv_DC	108.60°	69.62°	-54.80°	77.31°	126.89°	16.99Å	3.4
6cuh_BA	105.70°	69.71°	-56.90°	76.95°	129.69°	17.44Å	3.5

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	7.4
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	7.4
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	7.5
2dtg_CD	112.45°	70.45°	-56.63°	81.76°	125.38°	16.00Å	8.4
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	8.4

O / N

TCR Details:

Item	Info
VB chain	O
VA chain	N
VB IMGT details	TRBV9/TRBJ1
VA IMGT details	TRAV35/TRAJ53
Species	human

Antigen Details:

Item	Info
Antigen Chain	M
Antigen Type	Peptide
Antigen Organism	HUMAN HERPESVIRUS 5 STRAIN AD169
Antigen Sequence	VMAPRTLIL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	K \| L
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-E*0101

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	S	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	H	L	I	T	A	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	R	V	T	L	R	C	S
B25	B26	B27	B28	B29	B37	B38	B39
P	R	S	G	D	L	S	V
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	Q	Q	S	L	D
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	L	Q	F	L	I	Q
B56	B57	B58	B63	B64	B65	B66	B67
Y	Y	N	G	E	E	R	A
B68	B69	B70	B71	B72	B74	B75	B76
K	G	N	I	L	E	R	F
B77	B78	B79	B80	B81	B83	B84	B85
S	A	Q	Q	F	P	D	L
B86	B87	B88	B89	B90	B91	B92	B93
H	S	E	L	N	L	S	S
B94	B95	B96	B97	B98	B99	B100	B101
L	E	L	G	D	S	A	L
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	A	N
B110	B111	B111A	B112A	B112	B113	B114	B115
P	G	D	S	S	N	E	K
B116	B117	B118	B119	B120	B121	B122	B123
L	F	F	G	S	G	T	Q
B124	B125	B126	B127
L	S	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	D	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	Q	P	L	G	G
A112	A113	A114	A115	A116	A117	A118	A119
S	N	Y	K	L	T	F	G
A120	A121	A122	A123	A124	A125	A126	A127
K	G	T	L	L	T	V	N
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSANPGDSSNEKLF	None	15
CDRB2	YYNGEE	None	6
CDRB1	SGDLS	None	5
CDRA3	AGQPLGGSNYKLT	None	13
CDRA2	LYKAGEL	None	7
CDRA1	SIFNT	None	5

Orientation and docking angles:

Angle	Value
BC2	105.57°
BC1	70.97°
BA	-53.68°
AC2	78.48°
AC1	128.99°
dc	16.89Å
Docking angle	68.61°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5w1w_TS	105.55°	70.76°	-53.88°	77.65°	129.17°	16.68Å	0.9
5w1w_ED	105.81°	71.13°	-54.40°	77.86°	128.93°	16.65Å	1.0
5w1w_JI	106.10°	70.74°	-54.96°	77.08°	128.55°	16.78Å	2.0
3rgv_BA	105.45°	69.60°	-56.35°	79.16°	129.29°	17.99Å	3.3
6py2_ED	106.09°	73.09°	-52.34°	79.71°	126.93°	16.77Å	3.5

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	7.8
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	8.0
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	8.6
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	8.7
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	8.8

T / S

TCR Details:

Item	Info
VB chain	T
VA chain	S
VB IMGT details	TRBV9/TRBJ1
VA IMGT details	TRAV35/TRAJ53
Species	human

Antigen Details:

Item	Info
Antigen Chain	R
Antigen Type	Peptide
Antigen Organism	HUMAN HERPESVIRUS 5 STRAIN AD169
Antigen Sequence	VMAPRTLIL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	P \| Q
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-E*0101

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	S	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	H	L	I	T	A	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	R	V	T	L	R	C	S
B25	B26	B27	B28	B29	B37	B38	B39
P	R	S	G	D	L	S	V
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	Q	Q	S	L	D
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	L	Q	F	L	I	Q
B56	B57	B58	B63	B64	B65	B66	B67
Y	Y	N	G	E	E	R	A
B68	B69	B70	B71	B72	B74	B75	B76
K	G	N	I	L	E	R	F
B77	B78	B79	B80	B81	B83	B84	B85
S	A	Q	Q	F	P	D	L
B86	B87	B88	B89	B90	B91	B92	B93
H	S	E	L	N	L	S	S
B94	B95	B96	B97	B98	B99	B100	B101
L	E	L	G	D	S	A	L
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	A	N
B110	B111	B111A	B112A	B112	B113	B114	B115
P	G	D	S	S	N	E	K
B116	B117	B118	B119	B120	B121	B122	B123
L	F	F	G	S	G	T	Q
B124	B125	B126	B127
L	S	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	D	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	Q	P	L	G	G
A112	A113	A114	A115	A116	A117	A118	A119
S	N	Y	K	L	T	F	G
A120	A121	A122	A123	A124	A125	A126	A127
K	G	T	L	L	T	V	N
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSANPGDSSNEKLF	None	15
CDRB2	YYNGEE	None	6
CDRB1	SGDLS	None	5
CDRA3	AGQPLGGSNYKLT	None	13
CDRA2	LYKAGEL	None	7
CDRA1	SIFNT	None	5

Orientation and docking angles:

Angle	Value
BC2	107.45°
BC1	71.42°
BA	-56.95°
AC2	73.48°
AC1	128.04°
dc	16.54Å
Docking angle	59.85°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5w1w_ON	107.00°	70.84°	-56.72°	73.12°	128.77°	16.58Å	1.1
6dfw_FE	107.30°	70.29°	-58.74°	73.73°	127.12°	17.20Å	2.4
2p1y_Ee	104.20°	69.26°	-55.90°	73.75°	128.40°	17.20Å	4.1
3tjh_DC	106.75°	68.71°	-59.08°	75.44°	127.99°	17.46Å	4.1
2p1y_Gg	104.08°	69.35°	-55.78°	73.93°	128.57°	17.19Å	4.2

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4x4x_CD	112.33°	72.96°	-60.80°	78.66°	125.88°	15.67Å	8.6
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	8.8
4x4y_CD	112.91°	73.65°	-61.15°	79.25°	124.76°	15.70Å	9.9
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	9.9
1fj1_BA	111.06°	71.30°	-51.24°	79.34°	123.74°	16.01Å	9.9

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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