Details for 6rp9

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Structure information

Crystal Structure of the T-Cell Receptor Nye_S3 Bound to Hla a2*01-Sllmwitqv

Item	Info
PDB	6rp9
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	3.12Å
Number of TCRs	3

Paired chains information

This PDB has 3 TCR(s).

E / D

TCR Details:

Item	Info
VB chain	E
VA chain	D
VB IMGT details	TRBV7/TRBJ1
VA IMGT details	TRAV12/TRAJ49
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	HOMO SAPIENS
Antigen Sequence	SLLMWITQV
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
R	Y	K	V	T	K	R	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	D	V	A	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	V	S	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	A	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	P	E	F	L	T	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	N	Y	E	A	Q	Q	D
B68	B69	B70	B71	B72	B73	B74	B75
K	S	G	L	P	N	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	S	A	E	R	P	E	G
B85	B86	B87	B88	B89	B90	B91	B92
S	I	S	T	L	T	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	E	Q	R	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
M	Y	R	C	A	S	S	S
B109	B110	B111	B112	B113	B114	B115	B116
P	G	G	V	S	T	E	A
B117	B118	B119	B120	B121	B122	B123	B124
F	F	G	Q	G	T	R	L
B125	B126	B127
T	V	V

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	K	E	V	E	Q	N	S
A9	A10	A11	A12	A13	A14	A15	A16
G	P	L	S	V	P	E	G
A17	A18	A19	A20	A21	A22	A23	A24
A	I	A	S	L	N	C	T
A25	A26	A27	A28	A29	A36	A37	A38
Y	S	D	R	G	S	Q	S
A39	A40	A41	A42	A43	A44	A45	A46
F	F	W	Y	R	Q	Y	S
A47	A48	A49	A50	A51	A52	A53	A54
G	K	S	P	E	L	I	M
A55	A56	A57	A58	A63	A64	A65	A66
F	I	Y	S	N	G	D	K
A67	A68	A74	A75	A76	A77	A78	A79
E	D	G	R	F	T	A	Q
A80	A81	A82	A83	A84	A85	A86	A87
L	N	K	A	S	Q	Y	V
A88	A89	A90	A91	A92	A93	A94	A95
S	L	L	I	R	D	S	Q
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	S	A	T	Y	L
A104	A105	A106	A107	A108	A109	A110	A113
C	A	L	T	R	G	P	G
A114	A115	A116	A117	A118	A119	A120	A121
N	Q	F	Y	F	G	T	G
A122	A123	A124	A125	A126	A127	A128
T	S	L	T	V	I	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSSPGGVSTEAF	None	13
CDRB2	FNYEAQ	None	6
CDRB1	SGHVS	None	5
CDRA3	ALTRGPGNQFY	None	11
CDRA2	IYSNGD	None	6
CDRA1	DRGSQS	None	6

Orientation and docking angles:

Angle	Value
BC2	103.04°
BC1	70.63°
BA	-52.14°
AC2	77.43°
AC1	123.13°
dc	16.73Å
Docking angle	67.27°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2ak4_ED	102.11°	71.38°	-53.33°	76.15°	122.60°	16.24Å	2.2
2ak4_UT	103.37°	72.39°	-51.01°	76.50°	123.50°	16.10Å	2.4
2ak4_JI	101.70°	71.88°	-53.24°	76.45°	122.20°	16.27Å	2.6
3kxf_PN	103.18°	71.96°	-49.57°	76.28°	122.83°	16.19Å	3.2
3kxf_OM	101.60°	72.68°	-53.07°	76.04°	122.32°	16.17Å	3.2

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	7.1
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	7.3
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	7.3
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	8.3
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	8.8

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV7/TRBJ1
VA IMGT details	TRAV12/TRAJ49
Species	human

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	HOMO SAPIENS
Antigen Sequence	SLLMWITQV
Antigen Length	9

MHC details:

Item	Info
MHC Chain	F \| G
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
R	Y	K	V	T	K	R	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	D	V	A	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	V	S	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	A	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	P	E	F	L	T	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	N	Y	E	A	Q	Q	D
B68	B69	B70	B71	B72	B73	B74	B75
K	S	G	L	P	N	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	S	A	E	R	P	E	G
B85	B86	B87	B88	B89	B90	B91	B92
S	I	S	T	L	T	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	E	Q	R	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
M	Y	R	C	A	S	S	S
B109	B110	B111	B112	B113	B114	B115	B116
P	G	G	V	S	T	E	A
B117	B118	B119	B120	B121	B122	B123	B124
F	F	G	Q	G	T	R	L
B125	B126	B127
T	V	V

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	K	E	V	E	Q	N	S
A9	A10	A11	A12	A13	A14	A15	A16
G	P	L	S	V	P	E	G
A17	A18	A19	A20	A21	A22	A23	A24
A	I	A	S	L	N	C	T
A25	A26	A27	A28	A29	A36	A37	A38
Y	S	D	R	G	S	Q	S
A39	A40	A41	A42	A43	A44	A45	A46
F	F	W	Y	R	Q	Y	S
A47	A48	A49	A50	A51	A52	A53	A54
G	K	S	P	E	L	I	M
A55	A56	A57	A58	A63	A64	A65	A66
F	I	Y	S	N	G	D	K
A67	A68	A74	A75	A76	A77	A78	A79
E	D	G	R	F	T	A	Q
A80	A81	A82	A83	A84	A85	A86	A87
L	N	K	A	S	Q	Y	V
A88	A89	A90	A91	A92	A93	A94	A95
S	L	L	I	R	D	S	Q
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	S	A	T	Y	L
A104	A105	A106	A107	A108	A109	A110	A113
C	A	L	T	R	G	P	G
A114	A115	A116	A117	A118	A119	A120	A121
N	Q	F	Y	F	G	T	G
A122	A123	A124	A125	A126	A127	A128
T	S	L	T	V	I	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSSPGGVSTEAF	None	13
CDRB2	FNYEAQ	None	6
CDRB1	SGHVS	None	5
CDRA3	ALTRGPGNQFY	None	11
CDRA2	IYSNGD	None	6
CDRA1	DRGSQS	None	6

Orientation and docking angles:

Angle	Value
BC2	103.58°
BC1	70.72°
BA	-51.57°
AC2	77.72°
AC1	123.05°
dc	16.75Å
Docking angle	64.20°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2ak4_UT	103.37°	72.39°	-51.01°	76.50°	123.50°	16.10Å	2.3
2ak4_ED	102.11°	71.38°	-53.33°	76.15°	122.60°	16.24Å	2.9
3kxf_PN	103.18°	71.96°	-49.57°	76.28°	122.83°	16.19Å	2.9
2ak4_JI	101.70°	71.88°	-53.24°	76.45°	122.20°	16.27Å	3.2
2ak4_PN	103.72°	72.78°	-49.18°	77.02°	123.05°	16.06Å	3.3

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	6.7
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	6.7
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	6.9
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	8.3
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	8.4

L / K

TCR Details:

Item	Info
VB chain	L
VA chain	K
VB IMGT details	TRBV7/TRBJ1
VA IMGT details	TRAV12/TRAJ49
Species	human

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
R	Y	K	V	T	K	R	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	D	V	A	L	R	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	I	S	G	H	V	S	L
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	A	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	G	P	E	F	L	T	Y
B56	B57	B58	B63	B64	B65	B66	B67
F	N	Y	E	A	Q	Q	D
B68	B69	B70	B71	B72	B73	B74	B75
K	S	G	L	P	N	D	R
B76	B77	B78	B79	B80	B81	B83	B84
F	S	A	E	R	P	E	G
B85	B86	B87	B88	B89	B90	B91	B92
S	I	S	T	L	T	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
R	T	E	Q	R	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
M	Y	R	C	A	S	S	S
B109	B110	B111	B112	B113	B114	B115	B116
P	G	G	V	S	T	E	A
B117	B118	B119	B120	B121	B122	B123	B124
F	F	G	Q	G	T	R	L
B125	B126	B127
T	V	V

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	K	E	V	E	Q	N	S
A9	A10	A11	A12	A13	A14	A15	A16
G	P	L	S	V	P	E	G
A17	A18	A19	A20	A21	A22	A23	A24
A	I	A	S	L	N	C	T
A25	A26	A27	A28	A29	A36	A37	A38
Y	S	D	R	G	S	Q	S
A39	A40	A41	A42	A43	A44	A45	A46
F	F	W	Y	R	Q	Y	S
A47	A48	A49	A50	A51	A52	A53	A54
G	K	S	P	E	L	I	M
A55	A56	A57	A58	A63	A64	A65	A66
F	I	Y	S	N	G	D	K
A67	A68	A74	A75	A76	A77	A78	A79
E	D	G	R	F	T	A	Q
A80	A81	A82	A83	A84	A85	A86	A87
L	N	K	A	S	Q	Y	V
A88	A89	A90	A91	A92	A93	A94	A95
S	L	L	I	R	D	S	Q
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	S	A	T	Y	L
A104	A105	A106	A107	A108	A109	A110	A113
C	A	L	T	R	G	P	G
A114	A115	A116	A117	A118	A119	A120	A121
N	Q	F	Y	F	G	T	G
A122	A123	A124	A125	A126	A127	A128
T	S	L	T	V	I	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSSPGGVSTEAF	None	13
CDRB2	FNYEAQ	None	6
CDRB1	SGHVS	None	5
CDRA3	ALTRGPGNQFY	None	11
CDRA2	IYSNGD	None	6
CDRA1	DRGSQS	None	6

Orientation and docking angles:

Angle	Value
BC2	103.10°
BC1	68.62°
BA	-47.13°
AC2	78.69°
AC1	128.90°
dc	17.46Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2vlj_ED	101.90°	68.47°	-48.75°	79.76°	127.73°	17.22Å	2.6
2vlk_ED	102.53°	68.22°	-50.04°	80.54°	127.47°	17.33Å	3.8
2vlr_JI	102.60°	68.26°	-50.48°	80.59°	128.66°	17.58Å	3.9
8eo8_JI	99.78°	66.91°	-47.34°	81.05°	128.79°	17.46Å	4.4
8enh_JI	100.05°	66.85°	-46.52°	81.14°	129.31°	17.53Å	4.4

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