Details for 5d2l

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Structure information

Crystal Structure of TCR C7 in complex with Hcmv Nlv Epitope Presented By HLA-A2

Item	Info
PDB	5d2l
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	3.511Å
Number of TCRs	4

Paired chains information

This PDB has 4 TCR(s).

F / E

TCR Details:

Item	Info
VB chain	F
VA chain	E
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV24/TRAJ49
Species	human

Antigen Details:

Item	Info
Antigen Chain	R
Antigen Type	Peptide
Antigen Organism	CYTOMEGALOVIRUS
Antigen Sequence	NLVPMVATV
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
G	A	G	V	S	Q	S	P
B9	B10	B11	B12	B13	B14	B15	B16
S	N	K	V	T	E	K	G
B17	B18	B19	B20	B21	B22	B23	B24
K	D	V	E	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	T	A	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	R	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	L	E	F	L	I	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	Q	G	N	S	A	P	D
B68	B69	B70	B71	B72	B73	B74	B75
K	S	G	L	P	S	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	S	A	E	R	T	G	E
B85	B86	B87	B88	B89	B90	B91	B92
S	V	S	T	L	T	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	Q	Q	E	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
V	Y	L	C	A	S	S	Q
B109	B110	B112	B113	B114	B115	B116	B117
T	Q	L	W	E	T	Q	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	L
B126	B127
V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSQTQLWETQY	None	12
CDRB2	FQGNSA	None	6
CDRB1	SGHTA	None	5
CDRA3	AFITGNQFY	None	9
CDRA2	MTLNGDE	None	7
CDRA1	SSNFYA	A1-6-E	6

Orientation and docking angles:

Angle	Value
BC2	105.77°
BC1	70.40°
BA	-57.72°
AC2	84.62°
AC1	126.01°
dc	16.69Å
Docking angle	27.70°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
8dnt_WV	106.15°	70.61°	-55.96°	82.31°	126.02°	16.99Å	3.0
5jzi_JI	103.64°	71.67°	-57.46°	81.83°	125.91°	16.54Å	3.7
5wki_ED	105.92°	71.26°	-58.68°	85.56°	129.52°	17.34Å	3.9
2e7l_DA	103.46°	72.58°	-58.01°	82.08°	125.57°	16.65Å	4.1
7su9_ED	106.07°	73.06°	-58.87°	84.52°	128.92°	16.85Å	4.1

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	5.1
2w60_AB	111.29°	72.16°	-56.81°	86.34°	123.74°	16.34Å	6.5
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	6.5
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	6.7
4hfu_HL	112.36°	71.78°	-58.26°	83.56°	125.23°	16.51Å	6.9

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV24/TRAJ49
Species	human

Antigen Details:

Item	Info
Antigen Chain	Q
Antigen Type	Peptide
Antigen Organism	CYTOMEGALOVIRUS
Antigen Sequence	NLVPMVATV
Antigen Length	9

MHC details:

Item	Info
MHC Chain	A \| B
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
G	A	G	V	S	Q	S	P
B9	B10	B11	B12	B13	B14	B15	B16
S	N	K	V	T	E	K	G
B17	B18	B19	B20	B21	B22	B23	B24
K	D	V	E	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	T	A	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	R	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	L	E	F	L	I	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	Q	G	N	S	A	P	D
B68	B69	B70	B71	B72	B73	B74	B75
K	S	G	L	P	S	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	S	A	E	R	T	G	E
B85	B86	B87	B88	B89	B90	B91	B92
S	V	S	T	L	T	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	Q	Q	E	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
V	Y	L	C	A	S	S	Q
B109	B110	B112	B113	B114	B115	B116	B117
T	Q	L	W	E	T	Q	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	L
B126	B127
V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSQTQLWETQY	None	12
CDRB2	FQGNSA	None	6
CDRB1	SGHTA	None	5
CDRA3	AFITGNQFY	None	9
CDRA2	MTLNGDE	None	7
CDRA1	SSNFYA	A1-6-E	6

Orientation and docking angles:

Angle	Value
BC2	106.93°
BC1	69.88°
BA	-60.61°
AC2	82.06°
AC1	124.04°
dc	16.53Å
Docking angle	29.44°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2nx5_UT	108.15°	71.49°	-60.47°	80.39°	125.18°	16.73Å	2.9
8dnt_BA	107.53°	70.59°	-59.08°	80.05°	125.21°	16.93Å	3.0
6xco_ED	106.09°	72.66°	-60.59°	81.18°	123.57°	16.24Å	3.1
4y1a_ED	106.20°	71.83°	-60.17°	79.83°	124.12°	16.73Å	3.1
4x6d_FE	104.85°	71.59°	-60.25°	80.32°	124.25°	16.92Å	3.3

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	4.7
5te6_HL	110.27°	71.02°	-62.37°	82.91°	121.25°	16.49Å	4.9
5te7_HL	110.03°	71.72°	-60.97°	83.32°	120.63°	16.37Å	5.1
4zxb_CD	111.97°	68.75°	-59.36°	81.84°	123.87°	16.46Å	5.3
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	5.5

L / K

TCR Details:

Item	Info
VB chain	L
VA chain	K
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV24/TRAJ49
Species	human

Antigen Details:

Item	Info
Antigen Chain	U
Antigen Type	Peptide
Antigen Organism	CYTOMEGALOVIRUS
Antigen Sequence	NLVPMVATV
Antigen Length	9

MHC details:

Item	Info
MHC Chain	G \| H
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
G	A	G	V	S	Q	S	P
B9	B10	B11	B12	B13	B14	B15	B16
S	N	K	V	T	E	K	G
B17	B18	B19	B20	B21	B22	B23	B24
K	D	V	E	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	T	A	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	R	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	L	E	F	L	I	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	Q	G	N	S	A	P	D
B68	B69	B70	B71	B72	B73	B74	B75
K	S	G	L	P	S	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	S	A	E	R	T	G	E
B85	B86	B87	B88	B89	B90	B91	B92
S	V	S	T	L	T	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	Q	Q	E	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
V	Y	L	C	A	S	S	Q
B109	B110	B112	B113	B114	B115	B116	B117
T	Q	L	W	E	T	Q	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	L
B126	B127
V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSQTQLWETQY	None	12
CDRB2	FQGNSA	None	6
CDRB1	SGHTA	None	5
CDRA3	AFITGNQFY	None	9
CDRA2	MTLNGDE	None	7
CDRA1	SSNFYA	A1-6-E	6

Orientation and docking angles:

Angle	Value
BC2	105.64°
BC1	70.74°
BA	-60.29°
AC2	80.84°
AC1	125.41°
dc	16.20Å
Docking angle	29.33°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4x6d_FE	104.85°	71.59°	-60.25°	80.32°	124.25°	16.92Å	1.9
2e7l_CB	104.72°	71.98°	-59.47°	80.72°	125.33°	16.84Å	1.9
4y1a_ED	106.20°	71.83°	-60.17°	79.83°	124.12°	16.73Å	2.1
6dfx_HG	104.84°	72.16°	-61.59°	81.40°	124.91°	16.54Å	2.2
3e3q_NM	103.85°	71.84°	-59.79°	81.45°	125.08°	16.85Å	2.4

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	6.3
5te6_HL	110.27°	71.02°	-62.37°	82.91°	121.25°	16.49Å	6.9
4zxb_CD	111.97°	68.75°	-59.36°	81.84°	123.87°	16.46Å	7.0
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	7.0
5te7_HL	110.03°	71.72°	-60.97°	83.32°	120.63°	16.37Å	7.1

P / O

TCR Details:

Item	Info
VB chain	P
VA chain	O
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV24/TRAJ49
Species	human

Antigen Details:

Item	Info
Antigen Chain	T
Antigen Type	Peptide
Antigen Organism	CYTOMEGALOVIRUS
Antigen Sequence	NLVPMVATV
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
G	A	G	V	S	Q	S	P
B9	B10	B11	B12	B13	B14	B15	B16
S	N	K	V	T	E	K	G
B17	B18	B19	B20	B21	B22	B23	B24
K	D	V	E	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	T	A	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	R	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	L	E	F	L	I	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	Q	G	N	S	A	P	D
B68	B69	B70	B71	B72	B73	B74	B75
K	S	G	L	P	S	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	S	A	E	R	T	G	E
B85	B86	B87	B88	B89	B90	B91	B92
S	V	S	T	L	T	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	Q	Q	E	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
V	Y	L	C	A	S	S	Q
B109	B110	B112	B113	B114	B115	B116	B117
T	Q	L	W	E	T	Q	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	L
B126	B127
V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSQTQLWETQY	None	12
CDRB2	FQGNSA	None	6
CDRB1	SGHTA	None	5
CDRA3	AFITGNQFY	None	9
CDRA2	MTLNGDE	None	7
CDRA1	SSNFYA	A1-6-E	6

Orientation and docking angles:

Angle	Value
BC2	106.49°
BC1	68.87°
BA	-58.46°
AC2	87.30°
AC1	127.13°
dc	17.44Å
Docking angle	28.35°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5wki_ED	105.92°	71.26°	-58.68°	85.56°	129.52°	17.34Å	3.9
4elm_HG	108.26°	71.40°	-61.17°	85.19°	127.00°	17.28Å	4.6
7n5c_ED	105.57°	71.00°	-59.85°	87.94°	130.75°	17.78Å	4.6
3pqy_ED	107.20°	69.52°	-58.40°	89.24°	131.57°	18.08Å	5.0
3pqy_TS	105.91°	69.89°	-57.66°	90.05°	131.38°	18.13Å	5.3

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	6.2
2w60_AB	111.29°	72.16°	-56.81°	86.34°	123.74°	16.34Å	7.1
4lsv_HL	112.42°	71.79°	-57.42°	87.34°	123.18°	16.92Å	7.8
4hfu_HL	112.36°	71.78°	-58.26°	83.56°	125.23°	16.51Å	7.8
3rpi_AB	111.40°	72.07°	-59.66°	84.25°	122.88°	16.71Å	8.0

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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