Details for 3skn

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Structure information

Crystal Structure of the Rl42 TCR Unliganded

Item	Info
PDB	3skn
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.9Å
Number of TCRs	4

Paired chains information

This PDB has 4 TCR(s).

B / A

TCR Details:

Item	Info
VB chain	B
VA chain	A
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ23
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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	R	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	L	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
Y	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	E	G	T	T	A
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	D	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	L	K	K	Q
B86	B87	B88	B89	B90	B91	B92	B93
N	F	L	L	G	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	G	Q	G
B110	B113	B114	B115	B116	B117	B118	B119
N	F	D	I	Q	Y	F	G
B120	B121	B122	B123	B124	B125	B126	B127
A	G	T	R	L	S	V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASGQGNFDIQY	None	11
CDRB2	SVGEGT	None	6
CDRB1	MNHEY	None	5
CDRA3	VVRAGKLI	None	8
CDRA2	VYSSG	None	5
CDRA1	NSASQS	None	6

Orientation and docking angles:

Angle	Value
BC2	103.01°
BC1	72.31°
BA	-64.04°
AC2	78.70°
AC1	122.99°
dc	16.96Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6lir_DC	103.55°	71.82°	-63.77°	78.79°	122.98°	16.32Å	1.0
5d7i_FE	103.88°	72.92°	-63.55°	78.71°	122.94°	16.52Å	1.3
4pjf_FE	103.84°	73.06°	-64.49°	79.39°	123.23°	16.53Å	1.5
5d7j_BA	103.93°	72.68°	-63.07°	79.25°	122.97°	16.57Å	1.5
4pjh_HG	103.29°	73.34°	-63.14°	79.06°	123.01°	16.41Å	1.5

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	6.9
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	6.9
3s96_AB	107.61°	73.57°	-66.51°	82.70°	120.78°	16.43Å	7.1
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	7.2
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	7.6

D / C

TCR Details:

Item	Info
VB chain	D
VA chain	C
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ23
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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	R	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	L	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
Y	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	E	G	T	T	A
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	D	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	L	K	K	Q
B86	B87	B88	B89	B90	B91	B92	B93
N	F	L	L	G	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	G	Q	G
B110	B113	B114	B115	B116	B117	B118	B119
N	F	D	I	Q	Y	F	G
B120	B121	B122	B123	B124	B125	B126	B127
A	G	T	R	L	S	V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASGQGNFDIQY	None	11
CDRB2	SVGEGT	None	6
CDRB1	MNHEY	None	5
CDRA3	VVRAGKLI	None	8
CDRA2	VYSSG	None	5
CDRA1	NSASQS	None	6

Orientation and docking angles:

Angle	Value
BC2	103.73°
BC1	73.20°
BA	-63.62°
AC2	75.26°
AC1	124.51°
dc	17.21Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6c68_DC	102.80°	73.30°	-62.91°	75.73°	125.94°	16.59Å	2.0
6uz1_ED	103.15°	73.02°	-61.74°	74.37°	123.46°	16.24Å	2.6
4x6b_DC	105.38°	72.98°	-64.44°	74.90°	122.21°	16.55Å	3.0
2xn9_BA	105.51°	72.32°	-61.82°	74.17°	124.46°	16.45Å	3.0
4grm_BA	104.75°	74.22°	-61.93°	76.60°	123.01°	16.23Å	3.2

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	5.6
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	7.7
4uim_AB	109.49°	71.42°	-65.63°	76.99°	119.77°	15.95Å	8.2
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	8.8
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	9.0

F / E

TCR Details:

Item	Info
VB chain	F
VA chain	E
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ23
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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	R	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	L	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
Y	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	E	G	T	T	A
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	D	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	L	K	K	Q
B86	B87	B88	B89	B90	B91	B92	B93
N	F	L	L	G	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	G	Q	G
B110	B113	B114	B115	B116	B117	B118	B119
N	F	D	I	Q	Y	F	G
B120	B121	B122	B123	B124	B125	B126	B127
A	G	T	R	L	S	V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASGQGNFDIQY	None	11
CDRB2	SVGEGT	None	6
CDRB1	MNHEY	None	5
CDRA3	VVRAGKLI	None	8
CDRA2	VYSSG	None	5
CDRA1	NSASQS	None	6

Orientation and docking angles:

Angle	Value
BC2	101.54°
BC1	70.96°
BA	-60.76°
AC2	82.11°
AC1	121.75°
dc	17.03Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4e41_ED	102.89°	73.20°	-60.14°	80.58°	122.38°	15.80Å	3.4
4pjh_FE	102.76°	73.09°	-60.93°	80.51°	123.55°	16.56Å	3.5
4pja_FE	102.90°	72.45°	-60.92°	80.29°	123.91°	16.77Å	3.5
3sjv_ON	102.32°	71.44°	-60.23°	85.39°	122.65°	17.19Å	3.6
7t2d_ED	102.83°	73.36°	-58.93°	80.80°	122.46°	16.08Å	3.7

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	8.0
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	8.3
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	8.6
5te7_HL	110.03°	71.72°	-60.97°	83.32°	120.63°	16.37Å	8.7
4hxb_HL	109.66°	72.24°	-59.19°	82.14°	119.35°	16.41Å	8.7

H / G

TCR Details:

Item	Info
VB chain	H
VA chain	G
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV12/TRAJ23
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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	R	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	L	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
Y	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	E	G	T	T	A
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	D	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	L	K	K	Q
B86	B87	B88	B89	B90	B91	B92	B93
N	F	L	L	G	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	G	Q	G
B110	B113	B114	B115	B116	B117	B118	B119
N	F	D	I	Q	Y	F	G
B120	B121	B122	B123	B124	B125	B126	B127
A	G	T	R	L	S	V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASGQGNFDIQY	None	11
CDRB2	SVGEGT	None	6
CDRB1	MNHEY	None	5
CDRA3	VVRAGKLI	None	8
CDRA2	VYSSG	None	5
CDRA1	NSASQS	None	6

Orientation and docking angles:

Angle	Value
BC2	101.86°
BC1	71.18°
BA	-62.76°
AC2	80.79°
AC1	123.11°
dc	17.06Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6ovn_BA	102.95°	70.15°	-62.53°	80.41°	124.25°	16.00Å	2.2
3sjv_JI	102.43°	71.16°	-60.88°	79.59°	124.34°	17.17Å	2.6
4pjf_HG	103.12°	73.06°	-61.65°	79.97°	123.64°	16.66Å	2.7
4pja_FE	102.90°	72.45°	-60.92°	80.29°	123.91°	16.77Å	2.7
6pue_ED	103.27°	72.77°	-61.54°	80.49°	124.09°	16.73Å	2.7

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	7.8
3s96_AB	107.61°	73.57°	-66.51°	82.70°	120.78°	16.43Å	7.9
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	8.7
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	8.8
5te6_HL	110.27°	71.02°	-62.37°	82.91°	121.25°	16.49Å	8.9

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