Details for 3kxf

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Structure information

Crystal Structure of Sb27 TCR in complex with the 'Restriction Triad' Mutant HLA-B*3508-13Mer

Item	Info
PDB	3kxf
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	3.1Å
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	Q
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-B3578:HLA-B3508

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B3	B4	B5	B6	B7	B8	B9	B10
G	V	T	Q	T	P	K	F
B11	B12	B13	B14	B15	B16	B17	B18
Q	V	L	K	T	G	Q	S
B19	B20	B21	B22	B23	B24	B25	B26
M	T	L	Q	C	A	Q	D
B27	B28	B29	B37	B38	B39	B40	B41
M	N	H	N	S	M	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	R	Q	D	P	G	M	G
B50	B51	B52	B53	B54	B55	B56	B57
L	R	L	I	Y	Y	S	A
B58	B63	B64	B65	B66	B67	B68	B69
S	E	G	T	T	D	K	G
B70	B71	B72	B74	B75	B76	B77	B78
E	V	P	N	G	Y	N	V
B79	B80	B81	B83	B84	B85	B86	B87
S	R	L	N	K	R	E	F
B88	B89	B90	B91	B92	B93	B94	B95
S	L	R	L	E	S	A	A
B96	B97	B98	B99	B100	B101	B102	B103
P	S	Q	T	S	V	Y	F
B104	B105	B106	B107	B108	B109	B110	B112
C	A	S	P	G	L	A	G
B113	B114	B115	B116	B117	B118	B119	B120
E	Y	E	Q	Y	F	G	P
B121	B122	B123	B124	B125	B126	B127
G	T	R	L	T	V	T

FASTA file

A2	A3	A4	A5	A6	A7	A8	A9
Q	K	V	T	Q	A	Q	T
A10	A11	A12	A13	A14	A15	A16	A17
E	I	S	V	V	E	D	E
A18	A19	A20	A21	A22	A23	A24	A25
D	V	T	L	D	C	V	Y
A26	A27	A28	A29	A30	A36	A37	A38
E	T	R	D	T	T	Y	Y
A39	A40	A41	A42	A43	A44	A45	A46
L	F	W	Y	K	Q	P	P
A47	A48	A49	A50	A51	A52	A53	A54
S	G	E	L	V	F	L	I
A55	A56	A57	A58	A59	A62	A63	A64
R	R	N	S	F	D	E	Q
A65	A66	A67	A68	A74	A75	A76	A77
N	E	I	S	G	R	Y	S
A78	A79	A80	A81	A82	A83	A84	A85
W	N	F	Q	K	S	T	S
A86	A87	A88	A89	A90	A91	A92	A93
S	F	N	F	T	I	T	A
A94	A95	A96	A97	A98	A99	A100	A101
S	Q	V	V	D	S	A	V
A102	A103	A104	A105	A106	A107	A108	A109
Y	F	C	A	L	S	G	F
A110	A112	A113	A114	A115	A116	A117	A118
Y	N	T	D	K	L	I	F
A119	A120	A121	A122	A123	A124	A125	A126
G	T	G	T	R	L	Q	V
A127	A128
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	101.47°
BC1	72.23°
BA	-53.55°
AC2	75.94°
AC1	122.08°
dc	16.11Å
Docking angle	69.89°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2ak4_JI	101.70°	71.88°	-53.24°	76.45°	122.20°	16.27Å	0.8
2ak4_ED	102.11°	71.38°	-53.33°	76.15°	122.60°	16.24Å	1.2
7r7z_BA	100.53°	71.60°	-53.55°	78.38°	120.55°	15.99Å	3.1
6rp9_ED	103.04°	70.63°	-52.14°	77.43°	123.13°	16.73Å	3.3
2ak4_UT	103.37°	72.39°	-51.01°	76.50°	123.50°	16.10Å	3.5

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	9.0
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	9.3
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	9.6
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	9.6
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	9.8

H / G

TCR Details:

Item	Info
VB chain	H
VA chain	G
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV19/TRAJ34
Species	human

Antigen Details:

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

MHC details:

Item	Info
MHC Chain	C \| F
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B3578:HLA-B3508

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B3	B4	B5	B6	B7	B8	B9	B10
G	V	T	Q	T	P	K	F
B11	B12	B13	B14	B15	B16	B17	B18
Q	V	L	K	T	G	Q	S
B19	B20	B21	B22	B23	B24	B25	B26
M	T	L	Q	C	A	Q	D
B27	B28	B29	B37	B38	B39	B40	B41
M	N	H	N	S	M	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	R	Q	D	P	G	M	G
B50	B51	B52	B53	B54	B55	B56	B57
L	R	L	I	Y	Y	S	A
B58	B63	B64	B65	B66	B67	B68	B69
S	E	G	T	T	D	K	G
B70	B71	B72	B74	B75	B76	B77	B78
E	V	P	N	G	Y	N	V
B79	B80	B81	B83	B84	B85	B86	B87
S	R	L	N	K	R	E	F
B88	B89	B90	B91	B92	B93	B94	B95
S	L	R	L	E	S	A	A
B96	B97	B98	B99	B100	B101	B102	B103
P	S	Q	T	S	V	Y	F
B104	B105	B106	B107	B108	B109	B110	B112
C	A	S	P	G	L	A	G
B113	B114	B115	B116	B117	B118	B119	B120
E	Y	E	Q	Y	F	G	P
B121	B122	B123	B124	B125	B126	B127
G	T	R	L	T	V	T

FASTA file

A2	A3	A4	A5	A6	A7	A8	A9
Q	K	V	T	Q	A	Q	T
A10	A11	A12	A13	A14	A15	A16	A17
E	I	S	V	V	E	D	E
A18	A19	A20	A21	A22	A23	A24	A25
D	V	T	L	D	C	V	Y
A26	A27	A28	A29	A30	A36	A37	A38
E	T	R	D	T	T	Y	Y
A39	A40	A41	A42	A43	A44	A45	A46
L	F	W	Y	K	Q	P	P
A47	A48	A49	A50	A51	A52	A53	A54
S	G	E	L	V	F	L	I
A55	A56	A57	A58	A59	A62	A63	A64
R	R	N	S	F	D	E	Q
A65	A66	A67	A68	A74	A75	A76	A77
N	E	I	S	G	R	Y	S
A78	A79	A80	A81	A82	A83	A84	A85
W	N	F	Q	K	S	T	S
A86	A87	A88	A89	A90	A91	A92	A93
S	F	N	F	T	I	T	A
A94	A95	A96	A97	A98	A99	A100	A101
S	Q	V	V	D	S	A	V
A102	A103	A104	A105	A106	A107	A108	A109
Y	F	C	A	L	S	G	F
A110	A112	A113	A114	A115	A116	A117	A118
Y	N	T	D	K	L	I	F
A119	A120	A121	A122	A123	A124	A125	A126
G	T	G	T	R	L	Q	V
A127	A128
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	100.74°
BC1	73.37°
BA	-52.52°
AC2	75.24°
AC1	121.80°
dc	16.00Å
Docking angle	67.02°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2ak4_JI	101.70°	71.88°	-53.24°	76.45°	122.20°	16.27Å	2.3
2ak4_ED	102.11°	71.38°	-53.33°	76.15°	122.60°	16.24Å	2.8
4jrx_ED	100.99°	73.66°	-50.19°	77.76°	123.06°	15.83Å	3.7
2ak4_UT	103.37°	72.39°	-51.01°	76.50°	123.50°	16.10Å	3.8
7r7z_BA	100.53°	71.60°	-53.55°	78.38°	120.55°	15.99Å	4.0

O / M

TCR Details:

Item	Info
VB chain	O
VA chain	M
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	I \| J
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B3578:HLA-B3508

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B3	B4	B5	B6	B7	B8	B9	B10
G	V	T	Q	T	P	K	F
B11	B12	B13	B14	B15	B16	B17	B18
Q	V	L	K	T	G	Q	S
B19	B20	B21	B22	B23	B24	B25	B26
M	T	L	Q	C	A	Q	D
B27	B28	B29	B37	B38	B39	B40	B41
M	N	H	N	S	M	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	R	Q	D	P	G	M	G
B50	B51	B52	B53	B54	B55	B56	B57
L	R	L	I	Y	Y	S	A
B58	B63	B64	B65	B66	B67	B68	B69
S	E	G	T	T	D	K	G
B70	B71	B72	B74	B75	B76	B77	B78
E	V	P	N	G	Y	N	V
B79	B80	B81	B83	B84	B85	B86	B87
S	R	L	N	K	R	E	F
B88	B89	B90	B91	B92	B93	B94	B95
S	L	R	L	E	S	A	A
B96	B97	B98	B99	B100	B101	B102	B103
P	S	Q	T	S	V	Y	F
B104	B105	B106	B107	B108	B109	B110	B112
C	A	S	P	G	L	A	G
B113	B114	B115	B116	B117	B118	B119	B120
E	Y	E	Q	Y	F	G	P
B121	B122	B123	B124	B125	B126	B127
G	T	R	L	T	V	T

FASTA file

A2	A3	A4	A5	A6	A7	A8	A9
Q	K	V	T	Q	A	Q	T
A10	A11	A12	A13	A14	A15	A16	A17
E	I	S	V	V	E	D	E
A18	A19	A20	A21	A22	A23	A24	A25
D	V	T	L	D	C	V	Y
A26	A27	A28	A29	A30	A36	A37	A38
E	T	R	D	T	T	Y	Y
A39	A40	A41	A42	A43	A44	A45	A46
L	F	W	Y	K	Q	P	P
A47	A48	A49	A50	A51	A52	A53	A54
S	G	E	L	V	F	L	I
A55	A56	A57	A58	A59	A62	A63	A64
R	R	N	S	F	D	E	Q
A65	A66	A67	A68	A74	A75	A76	A77
N	E	I	S	G	R	Y	S
A78	A79	A80	A81	A82	A83	A84	A85
W	N	F	Q	K	S	T	S
A86	A87	A88	A89	A90	A91	A92	A93
S	F	N	F	T	I	T	A
A94	A95	A96	A97	A98	A99	A100	A101
S	Q	V	V	D	S	A	V
A102	A103	A104	A105	A106	A107	A108	A109
Y	F	C	A	L	S	G	F
A110	A112	A113	A114	A115	A116	A117	A118
Y	N	T	D	K	L	I	F
A119	A120	A121	A122	A123	A124	A125	A126
G	T	G	T	R	L	Q	V
A127	A128
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	101.60°
BC1	72.68°
BA	-53.07°
AC2	76.04°
AC1	122.32°
dc	16.17Å
Docking angle	69.54°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2ak4_JI	101.70°	71.88°	-53.24°	76.45°	122.20°	16.27Å	0.9
2ak4_ED	102.11°	71.38°	-53.33°	76.15°	122.60°	16.24Å	1.5
2ak4_UT	103.37°	72.39°	-51.01°	76.50°	123.50°	16.10Å	3.0
6rp9_ED	103.04°	70.63°	-52.14°	77.43°	123.13°	16.73Å	3.2
7r7z_BA	100.53°	71.60°	-53.55°	78.38°	120.55°	15.99Å	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	8.9
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	9.2
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	9.4
4yfl_HL	109.78°	73.75°	-56.79°	79.59°	122.71°	16.13Å	9.7
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	9.9

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	T
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-B3578:HLA-B3508

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B3	B4	B5	B6	B7	B8	B9	B10
G	V	T	Q	T	P	K	F
B11	B12	B13	B14	B15	B16	B17	B18
Q	V	L	K	T	G	Q	S
B19	B20	B21	B22	B23	B24	B25	B26
M	T	L	Q	C	A	Q	D
B27	B28	B29	B37	B38	B39	B40	B41
M	N	H	N	S	M	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	R	Q	D	P	G	M	G
B50	B51	B52	B53	B54	B55	B56	B57
L	R	L	I	Y	Y	S	A
B58	B63	B64	B65	B66	B67	B68	B69
S	E	G	T	T	D	K	G
B70	B71	B72	B74	B75	B76	B77	B78
E	V	P	N	G	Y	N	V
B79	B80	B81	B83	B84	B85	B86	B87
S	R	L	N	K	R	E	F
B88	B89	B90	B91	B92	B93	B94	B95
S	L	R	L	E	S	A	A
B96	B97	B98	B99	B100	B101	B102	B103
P	S	Q	T	S	V	Y	F
B104	B105	B106	B107	B108	B109	B110	B112
C	A	S	P	G	L	A	G
B113	B114	B115	B116	B117	B118	B119	B120
E	Y	E	Q	Y	F	G	P
B121	B122	B123	B124	B125	B126	B127
G	T	R	L	T	V	T

FASTA file

A2	A3	A4	A5	A6	A7	A8	A9
Q	K	V	T	Q	A	Q	T
A10	A11	A12	A13	A14	A15	A16	A17
E	I	S	V	V	E	D	E
A18	A19	A20	A21	A22	A23	A24	A25
D	V	T	L	D	C	V	Y
A26	A27	A28	A29	A30	A36	A37	A38
E	T	R	D	T	T	Y	Y
A39	A40	A41	A42	A43	A44	A45	A46
L	F	W	Y	K	Q	P	P
A47	A48	A49	A50	A51	A52	A53	A54
S	G	E	L	V	F	L	I
A55	A56	A57	A58	A59	A62	A63	A64
R	R	N	S	F	D	E	Q
A65	A66	A67	A68	A74	A75	A76	A77
N	E	I	S	G	R	Y	S
A78	A79	A80	A81	A82	A83	A84	A85
W	N	F	Q	K	S	T	S
A86	A87	A88	A89	A90	A91	A92	A93
S	F	N	F	T	I	T	A
A94	A95	A96	A97	A98	A99	A100	A101
S	Q	V	V	D	S	A	V
A102	A103	A104	A105	A106	A107	A108	A109
Y	F	C	A	L	S	G	F
A110	A112	A113	A114	A115	A116	A117	A118
Y	N	T	D	K	L	I	F
A119	A120	A121	A122	A123	A124	A125	A126
G	T	G	T	R	L	Q	V
A127	A128
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	103.18°
BC1	71.96°
BA	-49.57°
AC2	76.28°
AC1	122.83°
dc	16.19Å
Docking angle	67.86°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2ak4_PN	103.72°	72.78°	-49.18°	77.02°	123.05°	16.06Å	1.3
2ak4_UT	103.37°	72.39°	-51.01°	76.50°	123.50°	16.10Å	1.7
6rp9_JI	103.58°	70.72°	-51.57°	77.72°	123.05°	16.75Å	2.9
6rp9_ED	103.04°	70.63°	-52.14°	77.43°	123.13°	16.73Å	3.2
4jrx_ED	100.99°	73.66°	-50.19°	77.76°	123.06°	15.83Å	3.2

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	8.0
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	8.7
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	8.7

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Item	Link
IMGT-numbered structure	Link
Non-annotated structure from the PDB	Link
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Link in the PDB	Link