Details for 2ak4

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Structure information

Crystal Structure of Sb27 TCR in complex with HLA-B*3508-13Mer Peptide

Item	Info
PDB	2ak4
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	TRAV19/TRAJ34
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	LPEPLPQGQLTAY
Antigen Length	13

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*3508

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	N	S	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	Y	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	A	S	E	G	T	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	L	N	K	R
B86	B87	B88	B89	B90	B91	B92	B93
E	F	S	L	R	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	P	G	L
B110	B112	B113	B114	B115	B116	B117	B118
A	G	E	Y	E	Q	Y	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	T	V
B127
T

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
A	Q	K	V	T	Q	A	Q
A9	A10	A11	A12	A13	A14	A15	A16
T	E	I	S	V	V	E	K
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	T	L	D	C	V
A25	A26	A27	A28	A29	A30	A36	A37
Y	E	T	R	D	T	T	Y
A38	A39	A40	A41	A42	A43	A44	A45
Y	L	F	W	Y	K	Q	P
A46	A47	A48	A49	A50	A51	A52	A53
P	S	G	E	L	V	F	L
A54	A55	A56	A57	A58	A59	A62	A63
I	R	R	N	S	F	D	E
A64	A65	A66	A67	A68	A74	A75	A76
Q	N	E	I	S	G	R	Y
A77	A78	A79	A80	A81	A82	A83	A84
S	W	N	F	Q	K	S	T
A85	A86	A87	A88	A89	A90	A91	A92
S	S	F	N	F	T	I	T
A93	A94	A95	A96	A97	A98	A99	A100
A	S	Q	V	V	D	S	A
A101	A102	A103	A104	A105	A106	A107	A108
V	Y	F	C	A	L	S	G
A109	A110	A112	A113	A114	A115	A116	A117
F	Y	N	T	D	K	L	I
A118	A119	A120	A121	A122	A123	A124	A125
F	G	T	G	T	R	L	Q
A126	A127	A128
V	F	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASPGLAGEYEQY	None	12
CDRB2	SASEGT	None	6
CDRB1	MNHNS	None	5
CDRA3	ALSGFYNTDKLI	A3-12-B	12
CDRA2	RNSFDEQN	None	8
CDRA1	TRDTTYY	None	7

Orientation and docking angles:

Angle	Value
BC2	102.11°
BC1	71.38°
BA	-53.33°
AC2	76.15°
AC1	122.60°
dc	16.24Å
Docking angle	71.11°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
3kxf_ED	101.47°	72.23°	-53.55°	75.94°	122.08°	16.11Å	1.2
3kxf_OM	101.60°	72.68°	-53.07°	76.04°	122.32°	16.17Å	1.5
6rp9_ED	103.04°	70.63°	-52.14°	77.43°	123.13°	16.73Å	2.2
3kxf_HG	100.74°	73.37°	-52.52°	75.24°	121.80°	16.00Å	2.8
6rp9_JI	103.58°	70.72°	-51.57°	77.72°	123.05°	16.75Å	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	8.4
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	8.7
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	8.8
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	8.9
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	9.4

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV19/TRAJ34
Species	human

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	LPEPLPQGQLTAY
Antigen Length	13

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*3508

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	N	S	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	Y	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	A	S	E	G	T	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	L	N	K	R
B86	B87	B88	B89	B90	B91	B92	B93
E	F	S	L	R	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	P	G	L
B110	B112	B113	B114	B115	B116	B117	B118
A	G	E	Y	E	Q	Y	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	T	V
B127
T

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
A	Q	K	V	T	Q	A	Q
A9	A10	A11	A12	A13	A14	A15	A16
T	E	I	S	V	V	E	K
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	T	L	D	C	V
A25	A26	A27	A28	A29	A30	A36	A37
Y	E	T	R	D	T	T	Y
A38	A39	A40	A41	A42	A43	A44	A45
Y	L	F	W	Y	K	Q	P
A46	A47	A48	A49	A50	A51	A52	A53
P	S	G	E	L	V	F	L
A54	A55	A56	A57	A58	A59	A62	A63
I	R	R	N	S	F	D	E
A64	A65	A66	A67	A68	A74	A75	A76
Q	N	E	I	S	G	R	Y
A77	A78	A79	A80	A81	A82	A83	A84
S	W	N	F	Q	K	S	T
A85	A86	A87	A88	A89	A90	A91	A92
S	S	F	N	F	T	I	T
A93	A94	A95	A96	A97	A98	A99	A100
A	S	Q	V	V	D	S	A
A101	A102	A103	A104	A105	A106	A107	A108
V	Y	F	C	A	L	S	G
A109	A110	A112	A113	A114	A115	A116	A117
F	Y	N	T	D	K	L	I
A118	A119	A120	A121	A122	A123	A124	A125
F	G	T	G	T	R	L	Q
A126	A127	A128
V	F	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASPGLAGEYEQY	None	12
CDRB2	SASEGT	None	6
CDRB1	MNHNS	None	5
CDRA3	ALSGFYNTDKLI	A3-12-B	12
CDRA2	RNSFDEQN	None	8
CDRA1	TRDTTYY	None	7

Orientation and docking angles:

Angle	Value
BC2	101.70°
BC1	71.88°
BA	-53.24°
AC2	76.45°
AC1	122.20°
dc	16.27Å
Docking angle	70.59°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
3kxf_ED	101.47°	72.23°	-53.55°	75.94°	122.08°	16.11Å	0.8
3kxf_OM	101.60°	72.68°	-53.07°	76.04°	122.32°	16.17Å	0.9
3kxf_HG	100.74°	73.37°	-52.52°	75.24°	121.80°	16.00Å	2.3
6rp9_ED	103.04°	70.63°	-52.14°	77.43°	123.13°	16.73Å	2.6
7r7z_BA	100.53°	71.60°	-53.55°	78.38°	120.55°	15.99Å	2.8

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	8.4
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	8.8
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	9.1
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	9.1
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	9.6

P / N

TCR Details:

Item	Info
VB chain	P
VA chain	N
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV19/TRAJ34
Species	human

Antigen Details:

Item	Info
Antigen Chain	M
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	LPEPLPQGQLTAY
Antigen Length	13

MHC details:

Item	Info
MHC Chain	K \| L
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*3508

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	N	S	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	Y	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	A	S	E	G	T	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	L	N	K	R
B86	B87	B88	B89	B90	B91	B92	B93
E	F	S	L	R	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	P	G	L
B110	B112	B113	B114	B115	B116	B117	B118
A	G	E	Y	E	Q	Y	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	T	V
B127
T

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
A	Q	K	V	T	Q	A	Q
A9	A10	A11	A12	A13	A14	A15	A16
T	E	I	S	V	V	E	K
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	T	L	D	C	V
A25	A26	A27	A28	A29	A30	A36	A37
Y	E	T	R	D	T	T	Y
A38	A39	A40	A41	A42	A43	A44	A45
Y	L	F	W	Y	K	Q	P
A46	A47	A48	A49	A50	A51	A52	A53
P	S	G	E	L	V	F	L
A54	A55	A56	A57	A58	A59	A62	A63
I	R	R	N	S	F	D	E
A64	A65	A66	A67	A68	A74	A75	A76
Q	N	E	I	S	G	R	Y
A77	A78	A79	A80	A81	A82	A83	A84
S	W	N	F	Q	K	S	T
A85	A86	A87	A88	A89	A90	A91	A92
S	S	F	N	F	T	I	T
A93	A94	A95	A96	A97	A98	A99	A100
A	S	Q	V	V	D	S	A
A101	A102	A103	A104	A105	A106	A107	A108
V	Y	F	C	A	L	S	G
A109	A110	A112	A113	A114	A115	A116	A117
F	Y	N	T	D	K	L	I
A118	A119	A120	A121	A122	A123	A124	A125
F	G	T	G	T	R	L	Q
A126	A127	A128
V	F	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASPGLAGEYEQY	None	12
CDRB2	SASEGT	None	6
CDRB1	MNHNS	None	5
CDRA3	ALSGFYNTDKLI	A3-12-B	12
CDRA2	RNSFDEQN	None	8
CDRA1	TRDTTYY	None	7

Orientation and docking angles:

Angle	Value
BC2	103.72°
BC1	72.78°
BA	-49.18°
AC2	77.02°
AC1	123.05°
dc	16.06Å
Docking angle	66.83°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
3kxf_PN	103.18°	71.96°	-49.57°	76.28°	122.83°	16.19Å	1.3
4jrx_ED	100.99°	73.66°	-50.19°	77.76°	123.06°	15.83Å	3.1
6rp9_JI	103.58°	70.72°	-51.57°	77.72°	123.05°	16.75Å	3.3
6rp9_ED	103.04°	70.63°	-52.14°	77.43°	123.13°	16.73Å	3.8
1ymm_ED	102.52°	73.47°	-48.86°	81.32°	123.63°	15.82Å	4.6

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	7.4
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	8.2
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	8.3
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	9.8

U / T

TCR Details:

Item	Info
VB chain	U
VA chain	T
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV19/TRAJ34
Species	human

Antigen Details:

Item	Info
Antigen Chain	S
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	LPEPLPQGQLTAY
Antigen Length	13

MHC details:

Item	Info
MHC Chain	Q \| R
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*3508

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	N	S	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	Y	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	A	S	E	G	T	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	L	N	K	R
B86	B87	B88	B89	B90	B91	B92	B93
E	F	S	L	R	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	P	G	L
B110	B112	B113	B114	B115	B116	B117	B118
A	G	E	Y	E	Q	Y	F
B119	B120	B121	B122	B123	B124	B125	B126
G	P	G	T	R	L	T	V
B127
T

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
A	Q	K	V	T	Q	A	Q
A9	A10	A11	A12	A13	A14	A15	A16
T	E	I	S	V	V	E	K
A17	A18	A19	A20	A21	A22	A23	A24
E	D	V	T	L	D	C	V
A25	A26	A27	A28	A29	A30	A36	A37
Y	E	T	R	D	T	T	Y
A38	A39	A40	A41	A42	A43	A44	A45
Y	L	F	W	Y	K	Q	P
A46	A47	A48	A49	A50	A51	A52	A53
P	S	G	E	L	V	F	L
A54	A55	A56	A57	A58	A59	A62	A63
I	R	R	N	S	F	D	E
A64	A65	A66	A67	A68	A74	A75	A76
Q	N	E	I	S	G	R	Y
A77	A78	A79	A80	A81	A82	A83	A84
S	W	N	F	Q	K	S	T
A85	A86	A87	A88	A89	A90	A91	A92
S	S	F	N	F	T	I	T
A93	A94	A95	A96	A97	A98	A99	A100
A	S	Q	V	V	D	S	A
A101	A102	A103	A104	A105	A106	A107	A108
V	Y	F	C	A	L	S	G
A109	A110	A112	A113	A114	A115	A116	A117
F	Y	N	T	D	K	L	I
A118	A119	A120	A121	A122	A123	A124	A125
F	G	T	G	T	R	L	Q
A126	A127	A128
V	F	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASPGLAGEYEQY	None	12
CDRB2	SASEGT	None	6
CDRB1	MNHNS	None	5
CDRA3	ALSGFYNTDKLI	A3-12-B	12
CDRA2	RNSFDEQN	None	8
CDRA1	TRDTTYY	None	7

Orientation and docking angles:

Angle	Value
BC2	103.37°
BC1	72.39°
BA	-51.01°
AC2	76.50°
AC1	123.50°
dc	16.10Å
Docking angle	68.11°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
3kxf_PN	103.18°	71.96°	-49.57°	76.28°	122.83°	16.19Å	1.7
6rp9_JI	103.58°	70.72°	-51.57°	77.72°	123.05°	16.75Å	2.3
6rp9_ED	103.04°	70.63°	-52.14°	77.43°	123.13°	16.73Å	2.4
3kxf_OM	101.60°	72.68°	-53.07°	76.04°	122.32°	16.17Å	3.0
4jrx_ED	100.99°	73.66°	-50.19°	77.76°	123.06°	15.83Å	3.1

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	7.5
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	8.1
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	8.1
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	9.3
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	9.3

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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