Details for 2nx5

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Structure information

Crystal Structure of Els4 TCR Bound to HLA-B*3501 Presenting Ebv Peptide Eplpqgqltay at 1.7a

Item	Info
PDB	2nx5
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.7Å
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	TRBV10/TRBJ1
VA IMGT details	TRAV1/TRAJ6
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	EPLPQGQLTAY
Antigen Length	11

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*3501

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ATGTGDSNQPQH	None	12
CDRB2	SYGVKD	None	6
CDRB1	ENHRY	None	5
CDRA3	AVQASGGSYIPT	None	12
CDRA2	NVLDGL	None	6
CDRA1	TSGFNG	A1-6-F	6

Orientation and docking angles:

Angle	Value
BC2	108.26°
BC1	71.73°
BA	-60.30°
AC2	78.17°
AC1	124.77°
dc	16.81Å
Docking angle	56.70°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
8dnt_PM	107.67°	71.80°	-59.96°	78.60°	124.64°	16.70Å	0.8
7na5_ED	107.65°	72.03°	-60.43°	77.41°	125.33°	16.45Å	1.2
8dnt_IH	107.67°	72.60°	-59.28°	77.90°	124.75°	16.64Å	1.5
4ms8_DC	108.26°	71.77°	-62.08°	77.59°	124.79°	16.51Å	1.9
4mvb_DC	108.62°	71.71°	-62.21°	78.49°	125.19°	16.54Å	2.0

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3w14_PQ	112.54°	71.65°	-60.45°	80.80°	123.36°	16.03Å	5.3
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	5.4
4osu_HL	113.36°	71.18°	-59.13°	79.75°	123.24°	15.69Å	5.8
1fbi_QP	113.29°	73.42°	-61.95°	78.25°	123.04°	15.83Å	5.9
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	6.0

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV10/TRBJ1
VA IMGT details	TRAV1/TRAJ6
Species	human

Antigen Details:

Item	Info
Antigen Chain	M
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	EPLPQGQLTAY
Antigen Length	11

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*3501

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ATGTGDSNQPQH	None	12
CDRB2	SYGVKD	None	6
CDRB1	ENHRY	None	5
CDRA3	AVQASGGSYIPT	None	12
CDRA2	NVLDGL	None	6
CDRA1	TSGFNG	A1-6-F	6

Orientation and docking angles:

Angle	Value
BC2	107.82°
BC1	71.33°
BA	-61.50°
AC2	79.33°
AC1	124.52°
dc	16.64Å
Docking angle	58.90°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
3tf7_Ii	107.15°	71.55°	-61.98°	78.65°	125.58°	17.03Å	1.6
4mvb_DC	108.62°	71.71°	-62.21°	78.49°	125.19°	16.54Å	1.6
8dnt_PM	107.67°	71.80°	-59.96°	78.60°	124.64°	16.70Å	1.8
4ms8_DC	108.26°	71.77°	-62.08°	77.59°	124.79°	16.51Å	2.0
4g8f_BA	106.37°	71.74°	-62.87°	78.56°	124.53°	16.77Å	2.2

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	4.6
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	5.1
3w14_PQ	112.54°	71.65°	-60.45°	80.80°	123.36°	16.03Å	5.2
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	5.4
5te6_HL	110.27°	71.02°	-62.37°	82.91°	121.25°	16.49Å	5.5

P / N

TCR Details:

Item	Info
VB chain	P
VA chain	N
VB IMGT details	TRBV10/TRBJ1
VA IMGT details	TRAV1/TRAJ6
Species	human

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	EPLPQGQLTAY
Antigen Length	11

MHC details:

Item	Info
MHC Chain	K \| L
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*3501

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ATGTGDSNQPQH	None	12
CDRB2	SYGVKD	None	6
CDRB1	ENHRY	None	5
CDRA3	AVQASGGSYIPT	None	12
CDRA2	NVLDGL	None	6
CDRA1	TSGFNG	A1-6-F	6

Orientation and docking angles:

Angle	Value
BC2	108.96°
BC1	72.02°
BA	-62.01°
AC2	80.86°
AC1	124.76°
dc	16.37Å
Docking angle	61.58°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
3tf7_Gg	109.58°	71.38°	-62.20°	80.68°	127.04°	16.81Å	2.5
4mvb_DC	108.62°	71.71°	-62.21°	78.49°	125.19°	16.54Å	2.5
7t2b_ED	108.07°	71.08°	-64.40°	80.15°	124.66°	16.67Å	2.8
4elm_FE	108.59°	71.49°	-62.61°	82.96°	126.38°	16.99Å	2.9
3tf7_Cc	107.14°	72.79°	-61.91°	82.16°	126.70°	16.64Å	3.1

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	3.4
3w14_PQ	112.54°	71.65°	-60.45°	80.80°	123.36°	16.03Å	4.2
5te6_HL	110.27°	71.02°	-62.37°	82.91°	121.25°	16.49Å	4.4
1a4j_BA	111.30°	72.70°	-61.42°	83.26°	121.98°	16.50Å	4.4
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	4.6

U / T

TCR Details:

Item	Info
VB chain	U
VA chain	T
VB IMGT details	TRBV10/TRBJ1
VA IMGT details	TRAV1/TRAJ6
Species	human

Antigen Details:

Item	Info
Antigen Chain	S
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	EPLPQGQLTAY
Antigen Length	11

MHC details:

Item	Info
MHC Chain	Q \| R
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*3501

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ATGTGDSNQPQH	None	12
CDRB2	SYGVKD	None	6
CDRB1	ENHRY	None	5
CDRA3	AVQASGGSYIPT	None	12
CDRA2	NVLDGL	None	6
CDRA1	TSGFNG	A1-6-F	6

Orientation and docking angles:

Angle	Value
BC2	108.15°
BC1	71.49°
BA	-60.47°
AC2	80.39°
AC1	125.18°
dc	16.73Å
Docking angle	58.91°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
8dnt_BA	107.53°	70.59°	-59.08°	80.05°	125.21°	16.93Å	1.8
8dnt_PM	107.67°	71.80°	-59.96°	78.60°	124.64°	16.70Å	2.0
4y1a_ED	106.20°	71.83°	-60.17°	79.83°	124.12°	16.73Å	2.3
3e2h_CB	106.69°	73.41°	-60.12°	80.34°	124.94°	16.55Å	2.5
3tf7_Ii	107.15°	71.55°	-61.98°	78.65°	125.58°	17.03Å	2.6

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	4.4
3w14_PQ	112.54°	71.65°	-60.45°	80.80°	123.36°	16.03Å	4.8
4zxb_CD	111.97°	68.75°	-59.36°	81.84°	123.87°	16.46Å	5.2
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	5.5
2rcs_HL	112.26°	67.90°	-60.45°	80.52°	124.97°	16.31Å	5.5

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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