Details for 6rpb

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Structure information

Crystal Structure of the T-Cell Receptor Nye_S1 Bound to Hla a2*01-Sllmwitqv

Item	Info
PDB	6rpb
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.5Å
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/TRAJ6
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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	Q	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	Q	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
S	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	A	G	I	T	D
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	N	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	S	T	T	E
B86	B87	B88	B89	B90	B91	B92	B93
D	F	P	L	R	L	L	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	S	Y	L
B110	B112	B113	B114	B115	B116	B117	B118
N	R	D	S	A	L	D	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	T	V
B127
L

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	D	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	R	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	V	K	S	G	G	S
A114	A115	A116	A117	A118	A119	A120	A121
Y	I	P	T	F	G	R	G
A122	A123	A124	A125	A126	A127	A128
T	S	L	I	V	H	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSYLNRDSALD	None	12
CDRB2	SVGAGI	None	6
CDRB1	MNHEY	None	5
CDRA3	AVKSGGSYIPT	None	11
CDRA2	IYSDGD	None	6
CDRA1	DRGSQS	None	6

Orientation and docking angles:

Angle	Value
BC2	102.54°
BC1	70.25°
BA	-55.94°
AC2	79.68°
AC1	124.75°
dc	16.99Å
Docking angle	70.01°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2gj6_ED	100.49°	70.12°	-55.19°	80.35°	125.00°	17.00Å	2.3
7n6e_HG	102.63°	71.19°	-56.97°	81.44°	123.69°	16.62Å	2.5
4eup_HG	100.47°	71.36°	-55.50°	80.20°	125.61°	16.91Å	2.6
5yxu_GF	103.74°	70.63°	-55.17°	80.81°	126.54°	16.23Å	2.7
7amr_BA	100.70°	72.13°	-55.83°	80.70°	124.34°	16.62Å	2.9

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	7.0
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	7.4
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	7.6
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	8.1
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	8.4

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ6
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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	Q	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	Q	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
S	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	A	G	I	T	D
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	N	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	S	T	T	E
B86	B87	B88	B89	B90	B91	B92	B93
D	F	P	L	R	L	L	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	S	Y	L
B110	B112	B113	B114	B115	B116	B117	B118
N	R	D	S	A	L	D	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	T	V
B127
L

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	D	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	R	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	V	K	S	G	G	S
A114	A115	A116	A117	A118	A119	A120	A121
Y	I	P	T	F	G	R	G
A122	A123	A124	A125	A126	A127	A128
T	S	L	I	V	H	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSYLNRDSALD	None	12
CDRB2	SVGAGI	None	6
CDRB1	MNHEY	None	5
CDRA3	AVKSGGSYIPT	None	11
CDRA2	IYSDGD	None	6
CDRA1	DRGSQS	None	6

Orientation and docking angles:

Angle	Value
BC2	102.60°
BC1	70.52°
BA	-55.86°
AC2	80.51°
AC1	125.33°
dc	17.05Å
Docking angle	68.18°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5yxu_GF	103.74°	70.63°	-55.17°	80.81°	126.54°	16.23Å	2.0
5yxu_BA	103.19°	70.02°	-55.97°	81.28°	127.13°	16.34Å	2.2
5jzi_ED	102.19°	72.02°	-56.92°	81.33°	126.33°	16.63Å	2.3
7n6e_HG	102.63°	71.19°	-56.97°	81.44°	123.69°	16.62Å	2.3
2gj6_ED	100.49°	70.12°	-55.19°	80.35°	125.00°	17.00Å	2.3

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	6.9
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	7.6
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	7.9
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	7.9
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	8.4

O / N

TCR Details:

Item	Info
VB chain	O
VA chain	N
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ6
Species	human

Antigen Details:

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

MHC details:

Item	Info
MHC Chain	K \| L
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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	Q	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	Q	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
S	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	A	G	I	T	D
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	N	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	S	T	T	E
B86	B87	B88	B89	B90	B91	B92	B93
D	F	P	L	R	L	L	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	S	Y	L
B110	B112	B113	B114	B115	B116	B117	B118
N	R	D	S	A	L	D	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	T	V
B127
L

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	D	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	R	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	V	K	S	G	G	S
A114	A115	A116	A117	A118	A119	A120	A121
Y	I	P	T	F	G	R	G
A122	A123	A124	A125	A126	A127	A128
T	S	L	I	V	H	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSYLNRDSALD	None	12
CDRB2	SVGAGI	None	6
CDRB1	MNHEY	None	5
CDRA3	AVKSGGSYIPT	None	11
CDRA2	IYSDGD	None	6
CDRA1	DRGSQS	None	6

Orientation and docking angles:

Angle	Value
BC2	103.91°
BC1	70.36°
BA	-56.96°
AC2	80.73°
AC1	124.65°
dc	17.02Å
Docking angle	69.41°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5iw1_BA	104.32°	70.27°	-57.91°	80.58°	126.27°	17.21Å	1.9
7n6e_HG	102.63°	71.19°	-56.97°	81.44°	123.69°	16.62Å	2.0
5jzi_JI	103.64°	71.67°	-57.46°	81.83°	125.91°	16.54Å	2.3
7n6e_JI	103.86°	72.36°	-56.32°	81.13°	124.97°	16.31Å	2.3
6vth_BA	102.74°	71.64°	-57.94°	81.95°	125.13°	17.18Å	2.4

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	6.2
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	6.6
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	6.7
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	7.2

T / S

TCR Details:

Item	Info
VB chain	T
VA chain	S
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ6
Species	human

Antigen Details:

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

MHC details:

Item	Info
MHC Chain	P \| Q
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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	Q	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	Q	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
S	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	A	G	I	T	D
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	N	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	S	T	T	E
B86	B87	B88	B89	B90	B91	B92	B93
D	F	P	L	R	L	L	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	S	Y	L
B110	B112	B113	B114	B115	B116	B117	B118
N	R	D	S	A	L	D	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	T	V
B127
L

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	D	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	R	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	V	K	S	G	G	S
A114	A115	A116	A117	A118	A119	A120	A121
Y	I	P	T	F	G	R	G
A122	A123	A124	A125	A126	A127	A128
T	S	L	I	V	H	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSYLNRDSALD	None	12
CDRB2	SVGAGI	None	6
CDRB1	MNHEY	None	5
CDRA3	AVKSGGSYIPT	None	11
CDRA2	IYSDGD	None	6
CDRA1	DRGSQS	None	6

Orientation and docking angles:

Angle	Value
BC2	103.90°
BC1	70.20°
BA	-55.75°
AC2	81.00°
AC1	125.38°
dc	17.10Å
Docking angle	69.29°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5yxu_GF	103.74°	70.63°	-55.17°	80.81°	126.54°	16.23Å	1.6
5yxu_BA	103.19°	70.02°	-55.97°	81.28°	127.13°	16.34Å	2.1
7n6e_JI	103.86°	72.36°	-56.32°	81.13°	124.97°	16.31Å	2.4
5iw1_BA	104.32°	70.27°	-57.91°	80.58°	126.27°	17.21Å	2.4
5jzi_JI	103.64°	71.67°	-57.46°	81.83°	125.91°	16.54Å	2.5

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	6.0
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	6.5
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	6.8
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	7.2
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	7.2

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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