Details for 3kpr

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Structure information

Crystal Structure of the Lc13 TCR in complex with Hla B*4405 Bound to Eeylkawtf a Mimotope

Item	Info
PDB	3kpr
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.6Å
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	TRAV26/TRAJ52
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	EEYLKAWTF
Antigen Length	9

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*4405

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

A3	A4	A5	A6	A8	A9	A10	A11
K	T	T	Q	P	N	S	M
A12	A13	A14	A15	A16	A17	A18	A19
E	S	N	E	E	E	P	V
A20	A21	A22	A23	A24	A25	A26	A27
H	L	P	C	N	H	S	T
A28	A29	A30	A36	A37	A38	A39	A40
I	S	G	T	D	Y	I	H
A41	A42	A43	A44	A45	A46	A47	A48
W	Y	R	Q	L	P	S	Q
A49	A50	A51	A52	A53	A54	A55	A56
G	P	E	Y	V	I	H	G
A57	A58	A64	A65	A66	A67	A68	A74
L	T	S	N	V	N	N	R
A75	A76	A77	A78	A79	A80	A81	A82
M	A	S	L	A	I	A	E
A83	A84	A85	A86	A87	A88	A89	A90
D	R	K	S	S	T	L	I
A91	A92	A93	A94	A95	A96	A97	A98
L	H	R	A	T	L	R	D
A99	A100	A101	A102	A103	A104	A105	A106
A	A	V	Y	Y	C	I	L
A107	A108	A109	A110	A111	A112A	A112	A113
P	L	A	G	G	T	S	Y
A114	A115	A116	A117	A118	A119	A120	A121
G	K	L	T	F	G	Q	G
A122	A123	A124	A125	A126	A127	A128
T	I	L	T	V	H	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLGQAYEQY	None	11
CDRB2	FQNEAQ	None	6
CDRB1	SGHVS	None	5
CDRA3	ILPLAGGTSYGKLT	None	14
CDRA2	GLTSN	None	5
CDRA1	TISGTDY	None	7

Orientation and docking angles:

Angle	Value
BC2	108.37°
BC1	71.95°
BA	-62.50°
AC2	91.08°
AC1	133.35°
dc	17.66Å
Docking angle	41.62°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
3kps_ED	108.71°	71.81°	-63.92°	89.41°	132.56°	17.63Å	2.4
4gg6_FE	111.17°	73.07°	-62.86°	89.77°	131.55°	16.94Å	3.8
4gg6_HG	110.99°	73.29°	-63.02°	90.06°	131.30°	16.97Å	3.8
4z7v_HG	111.21°	73.03°	-62.36°	92.92°	131.88°	17.12Å	3.9
4z7v_FE	111.26°	73.06°	-61.69°	93.39°	131.70°	17.14Å	4.3

J / I

TCR Details:

Item	Info
VB chain	J
VA chain	I
VB IMGT details	TRBV7/TRBJ2
VA IMGT details	TRAV26/TRAJ52
Species	human

Antigen Details:

Item	Info
Antigen Chain	H
Antigen Type	Peptide
Antigen Organism	SYNTHETIC CONSTRUCT
Antigen Sequence	EEYLKAWTF
Antigen Length	9

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	MH1
MHC Species	human
MHC IMGT details	HLA-B*4405

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

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

FASTA file

A3	A4	A5	A6	A8	A9	A10	A11
K	T	T	Q	P	N	S	M
A12	A13	A14	A15	A16	A17	A18	A19
E	S	N	E	E	E	P	V
A20	A21	A22	A23	A24	A25	A26	A27
H	L	P	C	N	H	S	T
A28	A29	A30	A36	A37	A38	A39	A40
I	S	G	T	D	Y	I	H
A41	A42	A43	A44	A45	A46	A47	A48
W	Y	R	Q	L	P	S	Q
A49	A50	A51	A52	A53	A54	A55	A56
G	P	E	Y	V	I	H	G
A57	A58	A64	A65	A66	A67	A68	A74
L	T	S	N	V	N	N	R
A75	A76	A77	A78	A79	A80	A81	A82
M	A	S	L	A	I	A	E
A83	A84	A85	A86	A87	A88	A89	A90
D	R	K	S	S	T	L	I
A91	A92	A93	A94	A95	A96	A97	A98
L	H	R	A	T	L	R	D
A99	A100	A101	A102	A103	A104	A105	A106
A	A	V	Y	Y	C	I	L
A107	A108	A109	A110	A111	A112A	A112	A113
P	L	A	G	G	T	S	Y
A114	A115	A116	A117	A118	A119	A120	A121
G	K	L	T	F	G	Q	G
A122	A123	A124	A125	A126	A127	A128
T	I	L	T	V	H	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSLGQAYEQY	None	11
CDRB2	FQNEAQ	None	6
CDRB1	SGHVS	None	5
CDRA3	ILPLAGGTSYGKLT	None	14
CDRA2	GLTSN	None	5
CDRA1	TISGTDY	None	7

Orientation and docking angles:

Angle	Value
BC2	108.88°
BC1	73.13°
BA	-69.22°
AC2	86.90°
AC1	130.46°
dc	17.11Å
Docking angle	45.47°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
7ndu_ED	108.96°	74.94°	-65.93°	83.32°	131.18°	17.15Å	5.2
7ndq_ED	108.48°	75.73°	-66.33°	83.23°	130.91°	17.20Å	5.4
1mi5_ED	109.30°	72.73°	-63.43°	87.70°	131.17°	17.09Å	5.9
1kgc_ED	109.35°	71.85°	-63.15°	86.71°	130.57°	17.26Å	6.2
3kps_ED	108.71°	71.81°	-63.92°	89.41°	132.56°	17.63Å	6.4

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