Details for 4ei5

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Structure information

Crystal Structure of Xv19 TCR in complex with CD1D-Sulfatide C24:1

Item	Info
PDB	4ei5
Organism	CHIMERIC HOMO SAPIENS/MUS MUSCULUS
Method	X-RAY DIFFRACTION
Resolution	3.1Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

D / C

TCR Details:

Item	Info
VB chain	D
VA chain	C
VB IMGT details	TRBV3/TRBJ2
VA IMGT details	TRAV7/TRAJ26
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	A \| I
Antigen Type	Unknown
Antigen Organism	MUS MUSCULUS
Antigen name	(15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE; N-ACETYL-D-GLUCOSAMINE
Antigen residue	CIS \| NAG

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	CD1
MHC Species	mouse
MHC IMGT details	CD1D1*01

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
G	P	K	V	L	Q	I	P
B9	B10	B11	B12	B13	B14	B15	B16
S	H	Q	I	I	D	M	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	M	V	T	L	N	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	V	S	N	H	L	Y	F
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	K	Q	I	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	Q	M	E	F	L	V	N
B56	B57	B58	B63	B64	B65	B66	B67
F	Y	N	G	K	V	M	E
B68	B69	B70	B71	B72	B73	B74	B75
K	S	K	L	F	K	D	Q
B76	B77	B78	B79	B80	B81	B83	B84
F	S	V	E	R	P	D	G
B85	B86	B87	B88	B89	B90	B91	B92
S	Y	F	T	L	K	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
P	T	A	L	E	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
V	Y	F	C	A	S	S	F
B109	B110	B112	B113	B114	B115	B116	B117
W	G	A	Y	A	E	Q	F
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	T
B126	B127
V	L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	Q	K	V	Q	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
E	S	L	S	V	P	E	G
A17	A18	A19	A20	A21	A22	A23	A24
G	M	A	S	L	N	C	T
A25	A26	A27	A28	A29	A36	A37	A38
S	S	D	R	N	F	Q	Y
A39	A40	A41	A42	A43	A44	A45	A46
F	W	W	Y	R	Q	H	S
A47	A48	A49	A50	A51	A52	A53	A54
G	E	G	P	K	A	L	M
A55	A56	A57	A58	A63	A64	A65	A66
S	I	F	S	D	G	D	K
A67	A68	A74	A75	A76	A77	A78	A79
K	E	G	R	F	T	A	H
A80	A81	A82	A83	A84	A85	A86	A87
L	N	K	A	S	L	H	V
A88	A89	A90	A91	A92	A93	A94	A95
S	L	H	I	R	D	S	Q
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	S	A	L	Y	F
A104	A105	A106	A107	A108	A109	A110	A111
C	A	A	S	E	Q	N	N
A112	A113	A114	A115	A116	A117	A118	A119
Y	A	Q	G	L	T	F	G
A120	A121	A122	A123	A124	A125	A126	A127
L	G	T	R	V	S	V	F
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSFWGAYAEQF	None	12
CDRB2	FYNGKV	None	6
CDRB1	SNHLY	None	5
CDRA3	AASEQNNYAQGLT	None	13
CDRA2	IFSDGD	None	6
CDRA1	DRNFQY	None	6

Orientation and docking angles:

Angle	Value
BC2	107.74°
BC1	72.25°
BA	-65.83°
AC2	82.73°
AC1	124.47°
dc	16.93Å
Docking angle	73.81°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
8vz8_DC	105.58°	71.75°	-65.27°	80.76°	124.60°	16.54Å	3.0
4elk_BA	105.77°	71.69°	-67.56°	81.33°	124.76°	16.38Å	3.1
7t2b_ED	108.07°	71.08°	-64.40°	80.15°	124.66°	16.67Å	3.2
8i5d_BA	105.56°	71.73°	-65.25°	81.36°	126.32°	16.74Å	3.3
8vz9_DC	106.18°	72.14°	-63.32°	81.74°	125.40°	16.62Å	3.3

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	3.9
3s96_AB	107.61°	73.57°	-66.51°	82.70°	120.78°	16.43Å	4.0
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	5.4
5te6_HL	110.27°	71.02°	-62.37°	82.91°	121.25°	16.49Å	5.5
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	5.8

H / G

TCR Details:

Item	Info
VB chain	H
VA chain	G
VB IMGT details	TRBV3/TRBJ2
VA IMGT details	TRAV7/TRAJ26
Species	mouse

Antigen Details:

Item	Info
Antigen Chain	E \| K
Antigen Type	Unknown
Antigen Organism	MUS MUSCULUS
Antigen name	(15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE; N-ACETYL-D-GLUCOSAMINE
Antigen residue	CIS \| NAG

MHC details:

Item	Info
MHC Chain	E \| F
MHC Type	CD1
MHC Species	mouse
MHC IMGT details	CD1D1*01

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
G	P	K	V	L	Q	I	P
B9	B10	B11	B12	B13	B14	B15	B16
S	H	Q	I	I	D	M	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	M	V	T	L	N	C	D
B25	B26	B27	B28	B29	B37	B38	B39
P	V	S	N	H	L	Y	F
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	K	Q	I	L	G
B48	B49	B50	B51	B52	B53	B54	B55
Q	Q	M	E	F	L	V	N
B56	B57	B58	B63	B64	B65	B66	B67
F	Y	N	G	K	V	M	E
B68	B69	B70	B71	B72	B73	B74	B75
K	S	K	L	F	K	D	Q
B76	B77	B78	B79	B80	B81	B83	B84
F	S	V	E	R	P	D	G
B85	B86	B87	B88	B89	B90	B91	B92
S	Y	F	T	L	K	I	Q
B93	B94	B95	B96	B97	B98	B99	B100
P	T	A	L	E	D	S	A
B101	B102	B103	B104	B105	B106	B107	B108
V	Y	F	C	A	S	S	F
B109	B110	B112	B113	B114	B115	B116	B117
W	G	A	Y	A	E	Q	F
B118	B119	B120	B121	B122	B123	B124	B125
F	G	P	G	T	R	L	T
B126	B127
V	L

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
Q	Q	K	V	Q	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
E	S	L	S	V	P	E	G
A17	A18	A19	A20	A21	A22	A23	A24
G	M	A	S	L	N	C	T
A25	A26	A27	A28	A29	A36	A37	A38
S	S	D	R	N	F	Q	Y
A39	A40	A41	A42	A43	A44	A45	A46
F	W	W	Y	R	Q	H	S
A47	A48	A49	A50	A51	A52	A53	A54
G	E	G	P	K	A	L	M
A55	A56	A57	A58	A63	A64	A65	A66
S	I	F	S	D	G	D	K
A67	A68	A74	A75	A76	A77	A78	A79
K	E	G	R	F	T	A	H
A80	A81	A82	A83	A84	A85	A86	A87
L	N	K	A	S	L	H	V
A88	A89	A90	A91	A92	A93	A94	A95
S	L	H	I	R	D	S	Q
A96	A97	A98	A99	A100	A101	A102	A103
P	S	D	S	A	L	Y	F
A104	A105	A106	A107	A108	A109	A110	A111
C	A	A	S	E	Q	N	N
A112	A113	A114	A115	A116	A117	A118	A119
Y	A	Q	G	L	T	F	G
A120	A121	A122	A123	A124	A125	A126	A127
L	G	T	R	V	S	V	F
A128
P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSFWGAYAEQF	None	12
CDRB2	FYNGKV	None	6
CDRB1	SNHLY	None	5
CDRA3	AASEQNNYAQGLT	None	13
CDRA2	IFSDGD	None	6
CDRA1	DRNFQY	None	6

Orientation and docking angles:

Angle	Value
BC2	108.40°
BC1	72.98°
BA	-66.66°
AC2	80.45°
AC1	123.55°
dc	16.65Å
Docking angle	73.58°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
7t2b_TS	107.92°	71.65°	-66.21°	79.15°	123.48°	16.50Å	2.0
7t2b_ED	108.07°	71.08°	-64.40°	80.15°	124.66°	16.67Å	3.2
4elk_BA	105.77°	71.69°	-67.56°	81.33°	124.76°	16.38Å	3.4
2nw2_BA	105.62°	72.42°	-66.59°	78.59°	124.81°	16.89Å	3.6
8vz8_DC	105.58°	71.75°	-65.27°	80.76°	124.60°	16.54Å	3.6

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3s96_AB	107.61°	73.57°	-66.51°	82.70°	120.78°	16.43Å	3.7
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	4.1
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	4.3
3wii_IM	112.33°	71.31°	-64.39°	80.48°	121.86°	15.64Å	5.2
1ncc_HL	112.49°	72.25°	-63.92°	81.37°	121.51°	16.38Å	5.5

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