Details for 3sjv

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Structure information

Crystal Structure of the Rl42 TCR in complex with HLA-B8-Flr

Item	Info
PDB	3sjv
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	3.1Å
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	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ23
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	HUMAN HERPESVIRUS 4
Antigen Sequence	FLRGRAYGL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*0801

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASGQGNFDIQY	None	11
CDRB2	SVGEGT	None	6
CDRB1	MNHEY	None	5
CDRA3	VVRAGKLI	None	8
CDRA2	VYSSG	None	5
CDRA1	NSASQS	None	6

Orientation and docking angles:

Angle	Value
BC2	102.60°
BC1	70.79°
BA	-58.72°
AC2	86.15°
AC1	124.19°
dc	17.41Å
Docking angle	37.46°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5d7k_ED	101.16°	70.37°	-59.20°	86.27°	126.06°	17.13Å	2.5
3e3q_SR	100.83°	72.37°	-58.33°	83.18°	125.81°	16.62Å	4.2
5d2l_FE	105.77°	70.40°	-57.72°	84.62°	126.01°	16.69Å	4.2
6xc9_ED	103.47°	74.34°	-60.13°	84.82°	124.02°	15.88Å	4.4
6vth_BA	102.74°	71.64°	-57.94°	81.95°	125.13°	17.18Å	4.5

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	7.4
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	8.3
3mnv_DC	108.94°	70.99°	-55.77°	82.75°	119.97°	16.56Å	8.9
2w60_AB	111.29°	72.16°	-56.81°	86.34°	123.74°	16.34Å	9.1
5te7_HL	110.03°	71.72°	-60.97°	83.32°	120.63°	16.37Å	9.1

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ23
Species	human

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	HUMAN HERPESVIRUS 4
Antigen Sequence	FLRGRAYGL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*0801

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASGQGNFDIQY	None	11
CDRB2	SVGEGT	None	6
CDRB1	MNHEY	None	5
CDRA3	VVRAGKLI	None	8
CDRA2	VYSSG	None	5
CDRA1	NSASQS	None	6

Orientation and docking angles:

Angle	Value
BC2	102.43°
BC1	71.16°
BA	-60.88°
AC2	79.59°
AC1	124.34°
dc	17.17Å
Docking angle	37.78°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
8ye4_JI	102.33°	71.38°	-60.49°	78.95°	124.12°	17.10Å	0.8
8ye4_HG	102.01°	71.76°	-60.96°	79.15°	124.91°	17.07Å	1.0
4pja_FE	102.90°	72.45°	-60.92°	80.29°	123.91°	16.77Å	1.6
4h1l_HG	102.73°	72.35°	-61.12°	79.48°	125.31°	16.34Å	1.8
3rev_BA	101.29°	71.79°	-60.65°	78.74°	124.05°	16.31Å	1.8

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	8.7
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	8.8
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	8.9
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	8.9
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	9.1

O / N

TCR Details:

Item	Info
VB chain	O
VA chain	N
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ23
Species	human

Antigen Details:

Item	Info
Antigen Chain	M
Antigen Type	Peptide
Antigen Organism	HUMAN HERPESVIRUS 4
Antigen Sequence	FLRGRAYGL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	K \| L
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*0801

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASGQGNFDIQY	None	11
CDRB2	SVGEGT	None	6
CDRB1	MNHEY	None	5
CDRA3	VVRAGKLI	None	8
CDRA2	VYSSG	None	5
CDRA1	NSASQS	None	6

Orientation and docking angles:

Angle	Value
BC2	102.32°
BC1	71.44°
BA	-60.23°
AC2	85.39°
AC1	122.65°
dc	17.19Å
Docking angle	35.96°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6xc9_JI	103.16°	74.32°	-60.81°	84.60°	122.61°	15.91Å	3.4
3skn_FE	101.54°	70.96°	-60.76°	82.11°	121.75°	17.03Å	3.6
6xc9_ED	103.47°	74.34°	-60.13°	84.82°	124.02°	15.88Å	3.7
5d7k_ED	101.16°	70.37°	-59.20°	86.27°	126.06°	17.13Å	4.0
6p64_JI	102.94°	73.68°	-61.72°	87.44°	125.40°	16.77Å	4.4

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
5te7_HL	110.03°	71.72°	-60.97°	83.32°	120.63°	16.37Å	8.3
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	8.4
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	8.5
5te6_HL	110.27°	71.02°	-62.37°	82.91°	121.25°	16.49Å	8.7
4hxb_HL	109.66°	72.24°	-59.19°	82.14°	119.35°	16.41Å	8.8

T / S

TCR Details:

Item	Info
VB chain	T
VA chain	S
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ23
Species	human

Antigen Details:

Item	Info
Antigen Chain	R
Antigen Type	Peptide
Antigen Organism	HUMAN HERPESVIRUS 4
Antigen Sequence	FLRGRAYGL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	P \| Q
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*0801

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASGQGNFDIQY	None	11
CDRB2	SVGEGT	None	6
CDRB1	MNHEY	None	5
CDRA3	VVRAGKLI	None	8
CDRA2	VYSSG	None	5
CDRA1	NSASQS	None	6

Orientation and docking angles:

Angle	Value
BC2	102.96°
BC1	72.18°
BA	-61.91°
AC2	80.10°
AC1	125.49°
dc	16.90Å
Docking angle	38.91°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4h1l_HG	102.73°	72.35°	-61.12°	79.48°	125.31°	16.34Å	1.2
7zt9_ED	103.29°	71.54°	-62.82°	79.46°	124.99°	16.64Å	1.4
4pje_FE	103.32°	72.84°	-61.50°	80.80°	124.28°	16.77Å	1.6
6pue_ED	103.27°	72.77°	-61.54°	80.49°	124.09°	16.73Å	1.6
8ye4_HG	102.01°	71.76°	-60.96°	79.15°	124.91°	17.07Å	1.8

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	8.2
3s96_AB	107.61°	73.57°	-66.51°	82.70°	120.78°	16.43Å	8.6
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	8.7
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	8.8
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	8.9

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