Details for 6pud

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Structure information

Structure of Human Mait a-F7 TCR in complex with Human Mr1-5'Oh-Pentyl-5-Op-U

Item	Info
PDB	6pud
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	1.8Å
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	TRBV6/TRBJ2
VA IMGT details	TRAV1/TRAJ33
Species	human

Antigen Details:

Item	Info
Antigen Chain	C
Antigen Type	Hapten
Antigen Organism	HOMO SAPIENS
Antigen name	6-[(5-hydroxypentyl)amino]-5-[(E)-propylideneamino]pyrimidine-2,4(1H,3H)-dione
Antigen residue	OYD

MHC details:

Item	Info
MHC Chain	C \| F
MHC Type	MR1
MHC Species	human
MHC IMGT details	MR1*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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	Q	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	Q	C	A
B25	B26	B27	B28	B29	B37	B38	B39
Q	D	M	N	H	N	S	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
M	G	L	R	L	I	Y	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	A	S	E	G	T	T	D
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	N	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	L	N	K	R
B86	B87	B88	B89	B90	B91	B92	B93
E	F	S	L	R	L	E	S
B94	B95	B96	B97	B98	B99	B100	B101
A	A	P	S	Q	T	S	V
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	V	W
B110	B111	B112A	B112	B113	B114	B115	B116
T	G	E	G	S	G	E	L
B117	B118	B119	B120	B121	B122	B123	B124
F	F	G	E	G	S	R	L
B125	B126	B127
T	V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSVWTGEGSGELF	None	14
CDRB2	SASEGT	None	6
CDRB1	MNHNS	None	5
CDRA3	AVKDSNYQLI	None	10
CDRA2	NVLDGL	None	6
CDRA1	TSGFNG	A1-6-F	6

Orientation and docking angles:

Angle	Value
BC2	103.98°
BC1	73.06°
BA	-61.14°
AC2	80.62°
AC1	123.93°
dc	16.69Å
Docking angle	58.54°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6pul_ED	103.91°	73.05°	-61.18°	80.49°	123.92°	16.74Å	0.2
6pui_ED	104.03°	73.34°	-61.07°	80.52°	123.97°	16.69Å	0.3
5u17_GB	103.91°	73.21°	-60.92°	80.58°	123.99°	16.73Å	0.3
4nqd_HG	103.97°	73.02°	-60.93°	80.38°	124.10°	16.73Å	0.4
6pum_ED	103.73°	73.19°	-60.91°	80.68°	123.91°	16.79Å	0.4

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	6.8
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	7.0
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	7.2
3s96_AB	107.61°	73.57°	-66.51°	82.70°	120.78°	16.43Å	7.5
5te7_HL	110.03°	71.72°	-60.97°	83.32°	120.63°	16.37Å	7.5

H / G

TCR Details:

Item	Info
VB chain	H
VA chain	G
VB IMGT details	TRBV6/TRBJ2
VA IMGT details	TRAV1/TRAJ33
Species	human

Antigen Details:

Item	Info
Antigen Chain	A
Antigen Type	Hapten
Antigen Organism	HOMO SAPIENS
Antigen name	6-[(5-hydroxypentyl)amino]-5-[(E)-propylideneamino]pyrimidine-2,4(1H,3H)-dione
Antigen residue	OYD

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MR1
MHC Species	human
MHC IMGT details	MR1*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
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	Q	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	Q	C	A
B25	B26	B27	B28	B29	B37	B38	B39
Q	D	M	N	H	N	S	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
M	G	L	R	L	I	Y	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	A	S	E	G	T	T	D
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	N	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	L	N	K	R
B86	B87	B88	B89	B90	B91	B92	B93
E	F	S	L	R	L	E	S
B94	B95	B96	B97	B98	B99	B100	B101
A	A	P	S	Q	T	S	V
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	V	W
B110	B111	B112A	B112	B113	B114	B115	B116
T	G	E	G	S	G	E	L
B117	B118	B119	B120	B121	B122	B123	B124
F	F	G	E	G	S	R	L
B125	B126	B127
T	V	L

FASTA file

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

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSVWTGEGSGELF	None	14
CDRB2	SASEGT	None	6
CDRB1	MNHNS	None	5
CDRA3	AVKDSNYQLI	None	10
CDRA2	NVLDGL	None	6
CDRA1	TSGFNG	A1-6-F	6

Orientation and docking angles:

Angle	Value
BC2	104.03°
BC1	73.84°
BA	-64.65°
AC2	78.70°
AC1	122.77°
dc	16.49Å
Docking angle	61.77°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6pui_GB	104.00°	73.85°	-64.51°	78.70°	123.03°	16.48Å	0.3
5u6q_ED	103.89°	74.02°	-64.85°	78.65°	122.86°	16.42Å	0.3
6puj_GB	103.85°	73.94°	-64.58°	78.91°	122.95°	16.51Å	0.4
4nqe_ED	103.94°	73.92°	-64.91°	79.02°	122.86°	16.52Å	0.4
5u72_GB	104.12°	73.62°	-64.55°	78.41°	122.99°	16.48Å	0.4

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	6.0
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	6.3
5jue_HL	106.42°	70.98°	-68.16°	76.41°	119.66°	16.06Å	6.4
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	6.7
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	6.9

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