Details for 4mji

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Structure information

T Cell Response to a Hiv Reverse Transcriptase Epitope Presented By the Protective allele HLA-B*51:01

Item	Info
PDB	4mji
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.99Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

E / D

TCR Details:

Item	Info
VB chain	E
VA chain	D
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV17/TRAJ22
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen Sequence	TAFTIPSI
Antigen Length	8

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*5101

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLTGGGELF	None	11
CDRB2	FQGTGA	None	6
CDRB1	SGHTA	None	5
CDRA3	ATDDDSARQLT	None	11
CDRA2	IRSNERE	None	7
CDRA1	TSINN	None	5

Orientation and docking angles:

Angle	Value
BC2	108.26°
BC1	72.00°
BA	-69.04°
AC2	77.36°
AC1	126.13°
dc	16.30Å
Docking angle	44.03°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
7t2b_ON	108.26°	71.46°	-66.53°	77.16°	123.89°	16.44Å	3.4
4ei6_DC	105.99°	71.66°	-68.94°	79.57°	124.58°	16.60Å	3.6
7t2b_JI	108.80°	70.81°	-65.45°	77.16°	125.44°	16.56Å	3.9
4p4k_DC	106.63°	72.04°	-65.99°	75.64°	125.63°	16.65Å	3.9
3mff_BA	106.92°	71.88°	-68.46°	73.85°	127.42°	16.76Å	4.0

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1jv5_BA	111.45°	73.74°	-67.77°	74.39°	122.07°	15.49Å	6.4
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	6.9
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	7.2
5tbd_DG	112.72°	69.36°	-67.54°	80.19°	121.66°	16.24Å	7.6
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	8.0

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV17/TRAJ22
Species	human

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen Sequence	TAFTIPSI
Antigen Length	8

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*5101

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLTGGGELF	None	11
CDRB2	FQGTGA	None	6
CDRB1	SGHTA	None	5
CDRA3	ATDDDSARQLT	None	11
CDRA2	IRSNERE	None	7
CDRA1	TSINN	None	5

Orientation and docking angles:

Angle	Value
BC2	108.38°
BC1	72.09°
BA	-69.54°
AC2	77.32°
AC1	126.44°
dc	16.42Å
Docking angle	43.98°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4ei6_DC	105.99°	71.66°	-68.94°	79.57°	124.58°	16.60Å	3.8
7t2b_ON	108.26°	71.46°	-66.53°	77.16°	123.89°	16.44Å	4.0
3mff_BA	106.92°	71.88°	-68.46°	73.85°	127.42°	16.76Å	4.1
7t2b_JI	108.80°	70.81°	-65.45°	77.16°	125.44°	16.56Å	4.4
4p4k_DC	106.63°	72.04°	-65.99°	75.64°	125.63°	16.65Å	4.4

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1jv5_BA	111.45°	73.74°	-67.77°	74.39°	122.07°	15.49Å	6.6
1n4x_IM	107.07°	73.94°	-70.53°	72.40°	121.78°	15.58Å	7.3
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	7.3
5tbd_DG	112.72°	69.36°	-67.54°	80.19°	121.66°	16.24Å	7.8
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	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