Details for 3c5z

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Structure information

Crystal Structure of Mouse MHC Class Ii I-ab/3K Peptide complexed with Mouse TCR B3K506

Item	Info
PDB	3c5z
Organism	MUS MUSCULUS
Method	X-RAY DIFFRACTION
Resolution	2.55Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

B / A

TCR Details:

Item	Info
VB chain	B
VA chain	A
VB IMGT details	TRBV13/TRBJ1
VA IMGT details	TRAV6/TRAJ34
Species	mouse

MHC details:

Item	Info
MHC Chain	C \| D
MHC Type	MH2
MHC Species	mouse
MHC IMGT details	MH2-AA / H2-AB1*01

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASIDSSGNTLY	None	11
CDRB2	SYVADS	None	6
CDRB1	NNHDY	None	5
CDRA3	ALVISNTNKVV	None	11
CDRA2	ASRDKEK	None	7
CDRA1	ASGYPA	None	6

Orientation and docking angles:

Angle	Value
BC2	105.83°
BC1	72.54°
BA	-63.41°
AC2	72.83°
AC1	123.96°
dc	16.50Å
Docking angle	42.66°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2xn9_BA	105.51°	72.32°	-61.82°	74.17°	124.46°	16.45Å	2.2
4n0c_HG	106.16°	72.03°	-64.53°	73.99°	122.54°	17.21Å	2.3
2z35_BA	104.51°	72.08°	-64.38°	71.25°	124.26°	16.03Å	2.4
7f5k_DC	106.07°	71.79°	-62.77°	75.29°	123.23°	16.79Å	2.8
3c60_BA	107.87°	72.85°	-62.87°	74.17°	122.49°	16.41Å	2.9

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	3.7
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	7.5
1jv5_BA	111.45°	73.74°	-67.77°	74.39°	122.07°	15.49Å	7.7
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	7.7
4uil_HL	109.73°	69.62°	-65.41°	77.88°	119.52°	16.24Å	8.5

F / E

TCR Details:

Item	Info
VB chain	F
VA chain	E
VB IMGT details	TRBV13/TRBJ1
VA IMGT details	TRAV6/TRAJ34
Species	mouse

MHC details:

Item	Info
MHC Chain	G \| H
MHC Type	MH2
MHC Species	mouse
MHC IMGT details	MH2-AA / H2-AB1*01

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASIDSSGNTLY	None	11
CDRB2	SYVADS	None	6
CDRB1	NNHDY	None	5
CDRA3	ALVISNTNKVV	None	11
CDRA2	ASRDKEK	None	7
CDRA1	ASGYPA	None	6

Orientation and docking angles:

Angle	Value
BC2	105.85°
BC1	72.52°
BA	-63.47°
AC2	72.79°
AC1	123.93°
dc	16.50Å
Docking angle	49.25°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2z35_BA	104.51°	72.08°	-64.38°	71.25°	124.26°	16.03Å	2.3
4n0c_HG	106.16°	72.03°	-64.53°	73.99°	122.54°	17.21Å	2.3
2xn9_BA	105.51°	72.32°	-61.82°	74.17°	124.46°	16.45Å	2.3
7f5k_DC	106.07°	71.79°	-62.77°	75.29°	123.23°	16.79Å	2.8
3c60_BA	107.87°	72.85°	-62.87°	74.17°	122.49°	16.41Å	2.9

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	3.7
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	7.5
1jv5_BA	111.45°	73.74°	-67.77°	74.39°	122.07°	15.49Å	7.6
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	7.7
4uil_HL	109.73°	69.62°	-65.41°	77.88°	119.52°	16.24Å	8.5

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