Details for 6v80

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Structure information

Crystal Structure of Human CD1D Presenting alpha-Galactosylceramide in complex with Nkt12 TCR and Vhh Nanobody 1D12

Item	Info
PDB	6v80
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	3.53Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

D / C

TCR Details:

Item	Info
VB chain	D
VA chain	C
VB IMGT details	TRBV25/TRBJ2
VA IMGT details	TRAV10/TRAJ18
Species	human

Antigen Details:

Item	Info
Antigen Chain	A \| E
Antigen Type	Protein
Antigen Organism	homo sapiens ; lama glama
Antigen Sequence	QVQLVESGGGLVQAGGSLRLSCAASGSMFSDNVMGWYRQAPGKQRELVATIRTGGSTNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCRHTIPVPSTPYDYWGQGTQVTVSS/MQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGSLVPRGSGSRIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHGSGLNDIFEAQKIEWHEHHHHHH
Antigen Length	467

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	CD1
MHC Species	human
MHC IMGT details	CD1D*01

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B3	B4	B5	B6	B7	B8	B9	B10
D	I	Y	Q	T	P	R	Y
B11	B12	B13	B14	B15	B16	B17	B18
L	V	I	G	T	G	K	K
B19	B20	B21	B22	B23	B24	B25	B26
I	T	L	E	C	S	Q	T
B27	B28	B29	B37	B38	B39	B40	B41
M	G	H	D	K	M	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	Q	Q	D	P	G	M	E
B50	B51	B52	B53	B54	B55	B56	B57
L	H	L	I	H	Y	S	Y
B58	B63	B64	B65	B66	B67	B68	B69
G	V	N	S	T	E	K	G
B70	B71	B72	B74	B75	B76	B77	B78
D	L	S	S	E	S	T	V
B79	B80	B81	B83	B84	B85	B86	B87
S	R	I	R	T	E	H	F
B88	B89	B90	B91	B92	B93	B94	B95
P	L	T	L	E	S	A	R
B96	B97	B98	B99	B100	B101	B102	B103
P	S	H	T	S	Q	Y	L
B104	B105	B106	B107	B108	B109	B110	B112
C	A	S	T	S	R	R	G
B113	B114	B115	B116	B117	B118	B119	B120
S	Y	E	Q	Y	F	G	P
B121	B122	B123	B124	B125	B126	B127
G	T	R	L	T	V	T

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
K	N	Q	V	E	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	L	I	I	L	E	G
A17	A18	A19	A20	A21	A22	A23	A24
K	N	C	T	L	Q	C	N
A25	A26	A27	A28	A29	A36	A37	A38
Y	T	V	S	P	F	S	N
A39	A40	A41	A42	A43	A44	A45	A46
L	R	W	Y	K	Q	D	T
A47	A48	A49	A50	A51	A52	A53	A54
G	R	G	P	V	S	L	T
A55	A56	A57	A58	A59	A63	A64	A65
I	M	T	F	S	E	N	T
A66	A67	A68	A74	A75	A76	A77	A78
K	S	N	G	R	Y	T	A
A79	A80	A81	A82	A83	A84	A85	A86
T	L	D	A	D	T	K	Q
A87	A88	A89	A90	A91	A92	A93	A94
S	S	L	H	I	T	A	S
A95	A96	A97	A98	A99	A100	A101	A102
Q	L	S	D	S	A	S	Y
A103	A104	A105	A106	A107	A108	A109	A110
I	C	V	V	S	D	R	G
A111	A112	A113	A114	A115	A116	A117	A118
S	T	L	G	R	L	Y	F
A119	A120	A121	A122	A123	A124	A125	A126
G	R	G	T	Q	L	T	V
A127	A128
W	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASTSRRGSYEQY	None	12
CDRB2	SYGVNS	None	6
CDRB1	MGHDK	None	5
CDRA3	VVSDRGSTLGRLY	None	13
CDRA2	MTFSENT	None	7
CDRA1	VSPFSN	None	6

Orientation and docking angles:

Angle	Value
BC2	102.40°
BC1	73.29°
BA	-61.05°
AC2	82.36°
AC1	127.87°
dc	17.27Å
Docking angle	30.31°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
2po6_HG	101.02°	70.95°	-61.75°	83.95°	128.24°	17.22Å	3.2
6rpa_ED	102.31°	73.31°	-58.15°	80.86°	127.64°	17.41Å	3.3
7zt3_ED	102.64°	70.92°	-61.06°	82.28°	125.61°	16.96Å	3.3
3e3q_WV	100.93°	72.31°	-59.08°	82.20°	125.79°	16.55Å	3.4
3tzv_HG	101.12°	70.54°	-61.31°	83.81°	127.17°	17.14Å	3.4

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	9.9

I / H

TCR Details:

Item	Info
VB chain	I
VA chain	H
VB IMGT details	TRBV25/TRBJ2
VA IMGT details	TRAV10/TRAJ18
Species	human

Antigen Details:

Item	Info
Antigen Chain	F \| J
Antigen Type	Protein
Antigen Organism	homo sapiens ; lama glama
Antigen Sequence	QVQLVESGGGLVQAGGSLRLSCAASGSMFSDNVMGWYRQAPGKQRELVATIRTGGSTNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCRHTIPVPSTPYDYWGQGTQVTVSS/MQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGSLVPRGSGSRIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNHGSGLNDIFEAQKIEWHEHHHHHH
Antigen Length	467

MHC details:

Item	Info
MHC Chain	F \| G
MHC Type	CD1
MHC Species	human
MHC IMGT details	CD1D*01

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B3	B4	B5	B6	B7	B8	B9	B10
D	I	Y	Q	T	P	R	Y
B11	B12	B13	B14	B15	B16	B17	B18
L	V	I	G	T	G	K	K
B19	B20	B21	B22	B23	B24	B25	B26
I	T	L	E	C	S	Q	T
B27	B28	B29	B37	B38	B39	B40	B41
M	G	H	D	K	M	Y	W
B42	B43	B44	B45	B46	B47	B48	B49
Y	Q	Q	D	P	G	M	E
B50	B51	B52	B53	B54	B55	B56	B57
L	H	L	I	H	Y	S	Y
B58	B63	B64	B65	B66	B67	B68	B69
G	V	N	S	T	E	K	G
B70	B71	B72	B74	B75	B76	B77	B78
D	L	S	S	E	S	T	V
B79	B80	B81	B83	B84	B85	B86	B87
S	R	I	R	T	E	H	F
B88	B89	B90	B91	B92	B93	B94	B95
P	L	T	L	E	S	A	R
B96	B97	B98	B99	B100	B101	B102	B103
P	S	H	T	S	Q	Y	L
B104	B105	B106	B107	B108	B109	B110	B112
C	A	S	T	S	R	R	G
B113	B114	B115	B116	B117	B118	B119	B120
S	Y	E	Q	Y	F	G	P
B121	B122	B123	B124	B125	B126	B127
G	T	R	L	T	V	T

FASTA file

A1	A2	A3	A4	A5	A6	A7	A8
K	N	Q	V	E	Q	S	P
A9	A10	A11	A12	A13	A14	A15	A16
Q	S	L	I	I	L	E	G
A17	A18	A19	A20	A21	A22	A23	A24
K	N	C	T	L	Q	C	N
A25	A26	A27	A28	A29	A36	A37	A38
Y	T	V	S	P	F	S	N
A39	A40	A41	A42	A43	A44	A45	A46
L	R	W	Y	K	Q	D	T
A47	A48	A49	A50	A51	A52	A53	A54
G	R	G	P	V	S	L	T
A55	A56	A57	A58	A59	A63	A64	A65
I	M	T	F	S	E	N	T
A66	A67	A68	A74	A75	A76	A77	A78
K	S	N	G	R	Y	T	A
A79	A80	A81	A82	A83	A84	A85	A86
T	L	D	A	D	T	K	Q
A87	A88	A89	A90	A91	A92	A93	A94
S	S	L	H	I	T	A	S
A95	A96	A97	A98	A99	A100	A101	A102
Q	L	S	D	S	A	S	Y
A103	A104	A105	A106	A107	A108	A109	A110
I	C	V	V	S	D	R	G
A111	A112	A113	A114	A115	A116	A117	A118
S	T	L	G	R	L	Y	F
A119	A120	A121	A122	A123	A124	A125	A126
G	R	G	T	Q	L	T	V
A127	A128
W	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASTSRRGSYEQY	None	12
CDRB2	SYGVNS	None	6
CDRB1	MGHDK	None	5
CDRA3	VVSDRGSTLGRLY	None	13
CDRA2	MTFSENT	None	7
CDRA1	VSPFSN	None	6

Orientation and docking angles:

Angle	Value
BC2	101.62°
BC1	72.99°
BA	-64.05°
AC2	79.81°
AC1	127.48°
dc	17.14Å
Docking angle	31.01°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
4l9l_BA	102.30°	73.18°	-63.63°	80.48°	125.58°	16.78Å	2.2
3sdx_FE	101.12°	71.44°	-64.76°	81.96°	126.82°	17.19Å	2.9
3sdx_HG	100.74°	71.55°	-64.75°	81.91°	126.47°	17.26Å	3.0
4z7w_FE	104.51°	72.44°	-65.42°	79.27°	127.25°	16.80Å	3.3
3sjv_TS	102.96°	72.18°	-61.91°	80.10°	125.49°	16.90Å	3.3

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	9.8
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	9.9

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