Details for 4c56

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Structure information

X-Ray Structure of the complex Between Staphylococcal Enterotoxin B, T Cell Receptor and Major Histocompatibility complex Class Ii

Item	Info
PDB	4c56
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.9Å
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	TRBV19/TRBJ2
VA IMGT details	TRAV22/TRAJ40
Species	human

Antigen Details:

Item	Info
Antigen Chain	C \| F
Antigen Type	Protein
Antigen Organism	staphylococcus aureus ; influenza a virus
Antigen Sequence	PKYVKQNTLKLAT/SQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK
Antigen Length	252

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
D	G	G	I	T	Q	S	P
B9	B10	B11	B12	B13	B14	B15	B16
K	Y	L	F	R	K	E	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	N	V	T	L	S	C	E
B25	B26	B27	B28	B29	B37	B38	B39
Q	N	L	N	H	D	A	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
Q	G	L	R	L	I	Y	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	Q	I	V	N	D	F	Q
B68	B69	B70	B71	B72	B74	B75	B76
K	G	D	I	A	E	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
S	V	S	R	E	K	K	E
B86	B87	B88	B89	B90	B91	B92	B93
S	F	P	L	T	V	T	S
B94	B95	B96	B97	B98	B99	B100	B101
A	Q	K	N	P	T	A	F
B102	B103	B104	B105	B106	B107	B108	B109
Y	L	C	A	S	S	S	R
B110	B113	B114	B115	B116	B117	B118	B119
S	S	Y	E	Q	Y	F	G
B120	B121	B122	B123	B124	B125	B126	B127
P	G	T	R	L	T	V	T

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
G	I	Q	V	E	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
P	D	L	I	L	Q	E	G
A17	A18	A19	A20	A21	A22	A23	A24
A	N	S	T	L	R	C	N
A25	A26	A27	A28	A29	A37	A38	A39
F	S	D	S	V	N	N	L
A40	A41	A42	A43	A44	A45	A46	A47
Q	W	F	H	Q	N	P	W
A48	A49	A50	A51	A52	A53	A54	A55
G	Q	L	I	N	L	F	Y
A56	A57	A58	A64	A65	A66	A67	A68
I	P	S	G	T	K	Q	N
A74	A75	A76	A77	A78	A79	A80	A81
G	R	L	S	A	T	T	V
A82	A83	A84	A85	A86	A87	A88	A89
A	T	E	R	Y	S	L	L
A90	A91	A92	A93	A94	A95	A96	A97
Y	I	S	S	S	Q	T	T
A98	A99	A100	A101	A102	A103	A104	A105
D	S	G	V	Y	F	C	A
A106	A107	A108	A109	A110	A111	A112	A113
V	D	S	A	T	S	G	T
A114	A115	A116	A117	A118	A119	A120	A121
Y	K	Y	I	F	G	T	G
A122	A123	A124	A125	A126	A127
T	R	L	K	V	L

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSSRSSYEQY	None	11
CDRB2	SQIVND	None	6
CDRB1	LNHDA	None	5
CDRA3	AVDSATSGTYKYI	None	13
CDRA2	IPSGT	None	5
CDRA1	DSVNN	A1-5-B	5

Orientation and docking angles:

Angle	Value
BC2	102.63°
BC1	68.94°
BA	-53.41°
AC2	85.76°
AC1	124.42°
dc	16.28Å

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
1qrn_ED	100.87°	70.09°	-53.19°	83.07°	125.46°	17.07Å	3.7
5fk9_BA	104.25°	70.45°	-53.74°	83.05°	125.59°	16.11Å	3.7
1ao7_ED	101.22°	70.44°	-53.35°	82.76°	124.53°	17.28Å	3.8
4e42_DC	101.69°	69.47°	-52.06°	81.97°	124.55°	16.37Å	4.2
3pwp_ED	99.46°	70.45°	-54.01°	82.97°	125.10°	17.00Å	4.6

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	6.4
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	6.5
1cft_BA	107.61°	67.68°	-51.49°	84.71°	119.99°	16.31Å	7.1
1bog_BA	107.87°	66.84°	-51.21°	85.76°	120.10°	16.36Å	7.4
1cfn_BA	107.76°	67.31°	-50.48°	85.90°	120.10°	16.45Å	7.5

H / G

TCR Details:

Item	Info
VB chain	H
VA chain	G
VB IMGT details	TRBV19/TRBJ2
VA IMGT details	TRAV22/TRAJ40
Species	human

Antigen Details:

Item	Info
Antigen Chain	L \| I
Antigen Type	Protein
Antigen Organism	influenza a virus ; staphylococcus aureus
Antigen Sequence	PKYVKQNTLKLAT/SQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK
Antigen Length	252

MHC details:

Item	Info
MHC Chain	J \| K
MHC Type	MH2
MHC Species	human
MHC IMGT details	HLA-DRA0101 / HLA-DRB10101

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
D	G	G	I	T	Q	S	P
B9	B10	B11	B12	B13	B14	B15	B16
K	Y	L	F	R	K	E	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	N	V	T	L	S	C	E
B25	B26	B27	B28	B29	B37	B38	B39
Q	N	L	N	H	D	A	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
Q	G	L	R	L	I	Y	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	Q	I	V	N	D	F	Q
B68	B69	B70	B71	B72	B74	B75	B76
K	G	D	I	A	E	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
S	V	S	R	E	K	K	E
B86	B87	B88	B89	B90	B91	B92	B93
S	F	P	L	T	V	T	S
B94	B95	B96	B97	B98	B99	B100	B101
A	Q	K	N	P	T	A	F
B102	B103	B104	B105	B106	B107	B108	B109
Y	L	C	A	S	S	S	R
B110	B113	B114	B115	B116	B117	B118	B119
S	S	Y	E	Q	Y	F	G
B120	B121	B122	B123	B124	B125	B126	B127
P	G	T	R	L	T	V	T

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
G	I	Q	V	E	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
P	D	L	I	L	Q	E	G
A17	A18	A19	A20	A21	A22	A23	A24
A	N	S	T	L	R	C	N
A25	A26	A27	A28	A29	A37	A38	A39
F	S	D	S	V	N	N	L
A40	A41	A42	A43	A44	A45	A46	A47
Q	W	F	H	Q	N	P	W
A48	A49	A50	A51	A52	A53	A54	A55
G	Q	L	I	N	L	F	Y
A56	A57	A58	A64	A65	A66	A67	A68
I	P	S	G	T	K	Q	N
A74	A75	A76	A77	A78	A79	A80	A81
G	R	L	S	A	T	T	V
A82	A83	A84	A85	A86	A87	A88	A89
A	T	E	R	Y	S	L	L
A90	A91	A92	A93	A94	A95	A96	A97
Y	I	S	S	S	Q	T	T
A98	A99	A100	A101	A102	A103	A104	A105
D	S	G	V	Y	F	C	A
A106	A107	A108	A109	A110	A111	A112	A113
V	D	S	A	T	S	G	T
A114	A115	A116	A117	A118	A119	A120	A121
Y	K	Y	I	F	G	T	G
A122	A123	A124	A125	A126	A127
T	R	L	K	V	L

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSSRSSYEQY	None	11
CDRB2	SQIVND	None	6
CDRB1	LNHDA	None	5
CDRA3	AVDSATSGTYKYI	None	13
CDRA2	IPSGT	None	5
CDRA1	DSVNN	A1-5-B	5

Orientation and docking angles:

Angle	Value
BC2	103.95°
BC1	67.01°
BA	-55.96°
AC2	83.39°
AC1	124.61°
dc	16.20Å
Docking angle	64.87°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5nqk_BA	103.76°	68.20°	-57.08°	83.05°	122.37°	17.14Å	3.0
5nht_BA	104.13°	68.69°	-57.46°	82.69°	122.56°	16.86Å	3.2
2ial_BA	104.51°	67.15°	-56.72°	80.26°	124.94°	16.49Å	3.3
6rpb_TS	103.90°	70.20°	-55.75°	81.00°	125.38°	17.10Å	4.2
5fk9_BA	104.25°	70.45°	-53.74°	83.05°	125.59°	16.11Å	4.2

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	6.4
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	6.6
4ydl_HL	108.56°	70.76°	-54.72°	85.96°	123.49°	15.98Å	6.7
3mnz_BA	108.41°	71.26°	-53.27°	82.05°	121.70°	16.38Å	7.4
1cft_BA	107.61°	67.68°	-51.49°	84.71°	119.99°	16.31Å	7.5

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