Details for 4pjx

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Structure information

Structure of Human Mr1-ac-6-Fp in complex with Human Mait C-a11 TCR

Item	Info
PDB	4pjx
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.25Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

F / E

TCR Details:

Item	Info
VB chain	F
VA chain	E
VB IMGT details	TRBV6/TRBJ1
VA IMGT details	TRAV1/TRAJ33
Species	human

Antigen Details:

Item	Info
Antigen Chain	A \| A
Antigen Type	Unknown
Antigen Organism	HOMO SAPIENS
Antigen name	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL; N-(6-FORMYL-4-OXO-3,4-DIHYDROPTERIDIN-2-YL)ACETAMIDE
Antigen residue	B3P \| 30W

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	A	A
B110	B111	B112	B113	B114	B115	B116	B117
V	E	G	G	N	T	I	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	E	G	S	R	L	T
B126	B127
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	R	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	ASSAAVEGGNTIY	None	13
CDRB2	SASEGT	None	6
CDRB1	MNHNS	None	5
CDRA3	AVRDSNYQLI	None	10
CDRA2	NVLDGL	None	6
CDRA1	TSGFNG	A1-6-F	6

Orientation and docking angles:

Angle	Value
BC2	103.82°
BC1	72.61°
BA	-59.27°
AC2	80.63°
AC1	124.00°
dc	16.56Å
Docking angle	56.05°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
6pug_ED	103.58°	72.88°	-60.35°	80.20°	123.58°	16.68Å	1.3
5d7j_HG	104.60°	72.67°	-60.32°	80.40°	123.64°	16.71Å	1.4
5u1r_GB	103.39°	73.02°	-60.50°	80.34°	124.17°	16.71Å	1.4
6puk_ED	103.74°	72.74°	-60.61°	80.55°	124.32°	16.82Å	1.4
3e3q_ED	103.32°	72.06°	-59.90°	80.87°	125.10°	16.80Å	1.5

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	7.4
3bgf_BC	109.96°	71.90°	-55.10°	81.62°	123.51°	15.76Å	7.6
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	7.6
4hxb_HL	109.66°	72.24°	-59.19°	82.14°	119.35°	16.41Å	7.6
3mnw_BA	107.15°	71.13°	-53.34°	82.80°	121.51°	16.47Å	7.7

H / G

TCR Details:

Item	Info
VB chain	H
VA chain	G
VB IMGT details	TRBV6/TRBJ1
VA IMGT details	TRAV1/TRAJ33
Species	human

Antigen Details:

Item	Info
Antigen Chain	C \| C
Antigen Type	Unknown
Antigen Organism	HOMO SAPIENS
Antigen name	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL; N-(6-FORMYL-4-OXO-3,4-DIHYDROPTERIDIN-2-YL)ACETAMIDE
Antigen residue	B3P \| 30W

MHC details:

Item	Info
MHC Chain	C \| D
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	A	A
B110	B111	B112	B113	B114	B115	B116	B117
V	E	G	G	N	T	I	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	E	G	S	R	L	T
B126	B127
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	R	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	ASSAAVEGGNTIY	None	13
CDRB2	SASEGT	None	6
CDRB1	MNHNS	None	5
CDRA3	AVRDSNYQLI	None	10
CDRA2	NVLDGL	None	6
CDRA1	TSGFNG	A1-6-F	6

Orientation and docking angles:

Angle	Value
BC2	104.62°
BC1	73.12°
BA	-62.91°
AC2	78.97°
AC1	123.27°
dc	16.44Å
Docking angle	58.74°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4pj7_FE	104.93°	73.02°	-62.94°	79.01°	123.61°	16.69Å	0.5
5d5m_FE	104.63°	72.97°	-63.14°	79.47°	123.36°	16.58Å	0.6
5d7j_BA	103.93°	72.68°	-63.07°	79.25°	122.97°	16.57Å	0.9
5u1r_ED	104.10°	73.42°	-63.68°	78.68°	123.26°	16.55Å	1.0
4pja_HG	104.00°	72.79°	-63.36°	79.29°	123.58°	16.70Å	1.0

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	6.2
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	6.3
3s96_AB	107.61°	73.57°	-66.51°	82.70°	120.78°	16.43Å	6.5
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	6.7
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	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