Details for 2vlr

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Structure information

the Structural Dynamics and Energetics of an Immunodominant T-Cell Receptor are Programmed By Its Vbeta Domain

Item	Info
PDB	2vlr
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.3Å
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	TRBV19/TRBJ2
VA IMGT details	TRAV27/TRAJ42
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	UNIDENTIFIED INFLUENZA VIRUS
Antigen Sequence	GILGFVFTL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-A*0201

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSSRASYEQY	None	11
CDRB2	SQIVND	None	6
CDRB1	LNHDA	None	5
CDRA3	AGAGSQGNLI	A3-10-C	10
CDRA2	VVTGGEV	None	7
CDRA1	SVFSS	None	5

Orientation and docking angles:

Angle	Value
BC2	101.89°
BC1	68.24°
BA	-50.85°
AC2	80.78°
AC1	128.30°
dc	17.33Å
Docking angle	61.22°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5hhm_ED	101.72°	67.97°	-50.56°	81.00°	128.78°	16.94Å	0.8
5hhm_JI	102.11°	67.67°	-50.24°	81.42°	128.65°	17.00Å	1.2
2vlk_ED	102.53°	68.22°	-50.04°	80.54°	127.47°	17.33Å	1.3
5hho_ED	101.56°	67.45°	-50.20°	81.53°	128.75°	17.08Å	1.4
1oga_ED	101.63°	66.96°	-50.54°	80.21°	129.12°	17.20Å	1.7

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	9.7

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV19/TRBJ2
VA IMGT details	TRAV27/TRAJ42
Species	human

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	UNIDENTIFIED INFLUENZA VIRUS
Antigen Sequence	GILGFVFTL
Antigen Length	9

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-A*0201

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSSRASYEQY	None	11
CDRB2	SQIVND	None	6
CDRB1	LNHDA	None	5
CDRA3	AGAGSQGNLI	A3-10-C	10
CDRA2	VVTGGEV	None	7
CDRA1	SVFSS	None	5

Orientation and docking angles:

Angle	Value
BC2	102.60°
BC1	68.26°
BA	-50.48°
AC2	80.59°
AC1	128.66°
dc	17.58Å
Docking angle	61.78°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
5hhm_ED	101.72°	67.97°	-50.56°	81.00°	128.78°	16.94Å	1.2
2vlk_ED	102.53°	68.22°	-50.04°	80.54°	127.47°	17.33Å	1.3
5hhm_JI	102.11°	67.67°	-50.24°	81.42°	128.65°	17.00Å	1.3
5hho_ED	101.56°	67.45°	-50.20°	81.53°	128.75°	17.08Å	1.7
1oga_ED	101.63°	66.96°	-50.54°	80.21°	129.12°	17.20Å	1.8

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	9.7
1fj1_DC	109.78°	71.11°	-51.69°	80.11°	123.02°	16.12Å	9.8

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