Structure Viewer: 6qd6

> Structure details

Molecular Scaffolds Expand the Nanobody toolkit For Cryo-Em applications: Crystal Structure of Mb-Chopq-Nb207

PDB	6qd6
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
Method	X-RAY DIFFRACTION
Resolution	2.84Å
Number of Fvs	10
In complex	True
Light chain type
Has constant region	False

> Fv information

This PDB has 10 Fv(s).

Fv Details
Heavy chain	F
Light chain
Heavy subgroup	IGHV1
Light subgroup
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80	81	82	82A	82B	82C	83	84	85	86	87	88	89	90	91	92	93	94	95	96	97	98	99	100	100A	100B	100C	100D	100E	100F	100G	100H	100I	101	102	103	104	105	106	107	108	109	110	111	112	113
G	S	L	R	L	S	C	A	A	S	G	R	T	F	S	T	A	A	M	G	W	F	R	Q	A	P	G	K	E	R	D	F	V	A	G	I	Y	W	T	V	G	S	T	Y	Y	A	D	S	A	K	G	R	F	T	I	S	R	D	N	A	K	N	T	V	Y	L	Q	M	D	S	L	K	P	E	D	T	A	V	Y	Y	C	A	A	R	R	R	G	F	T	L	A	P	T	R	A	N	E	Y	D	Y	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen species	SYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1	GRTFSTA
CDRH2	YWTVGS
CDRH3	RRRGFTLAPTRANEYDY

Fv Details
Heavy chain	I
Light chain
Heavy subgroup	IGHV1
Light subgroup
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80	81	82	82A	82B	82C	83	84	85	86	87	88	89	90	91	92	93	94	95	96	97	98	99	100	100A	100B	100C	100D	100E	100F	100G	100H	100I	101	102	103	104	105	106	107	108	109	110	111	112	113
G	S	L	R	L	S	C	A	A	S	G	R	T	F	S	T	A	A	M	G	W	F	R	Q	A	P	G	K	E	R	D	F	V	A	G	I	Y	W	T	V	G	S	T	Y	Y	A	D	S	A	K	G	R	F	T	I	S	R	D	N	A	K	N	T	V	Y	L	Q	M	D	S	L	K	P	E	D	T	A	V	Y	Y	C	A	A	R	R	R	G	F	T	L	A	P	T	R	A	N	E	Y	D	Y	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen species	SYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1	GRTFSTA
CDRH2	YWTVGS
CDRH3	RRRGFTLAPTRANEYDY

Fv Details
Heavy chain	D
Light chain
Heavy subgroup	IGHV1
Light subgroup
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80	81	82	82A	82B	82C	83	84	85	86	87	88	89	90	91	92	93	94	95	96	97	98	99	100	100A	100B	100C	100D	100E	100F	100G	100H	100I	101	102	103	104	105	106	107	108	109	110	111	112	113
G	S	L	R	L	S	C	A	A	S	G	R	T	F	S	T	A	A	M	G	W	F	R	Q	A	P	G	K	E	R	D	F	V	A	G	I	Y	W	T	V	G	S	T	Y	Y	A	D	S	A	K	G	R	F	T	I	S	R	D	N	A	K	N	T	V	Y	L	Q	M	D	S	L	K	P	E	D	T	A	V	Y	Y	C	A	A	R	R	R	G	F	T	L	A	P	T	R	A	N	E	Y	D	Y	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen species	SYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1	GRTFSTA
CDRH2	YWTVGS
CDRH3	RRRGFTLAPTRANEYDY

Fv Details
Heavy chain	G
Light chain
Heavy subgroup	IGHV1
Light subgroup
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80	81	82	82A	82B	82C	83	84	85	86	87	88	89	90	91	92	93	94	95	96	97	98	99	100	100A	100B	100C	100D	100E	100F	100G	100H	100I	101	102	103	104	105	106	107	108	109	110	111	112	113
G	S	L	R	L	S	C	A	A	S	G	R	T	F	S	T	A	A	M	G	W	F	R	Q	A	P	G	K	E	R	D	F	V	A	G	I	Y	W	T	V	G	S	T	Y	Y	A	D	S	A	K	G	R	F	T	I	S	R	D	N	A	K	N	T	V	Y	L	Q	M	D	S	L	K	P	E	D	T	A	V	Y	Y	C	A	A	R	R	R	G	F	T	L	A	P	T	R	A	N	E	Y	D	Y	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen species	SYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1	GRTFSTA
CDRH2	YWTVGS
CDRH3	RRRGFTLAPTRANEYDY

Fv Details
Heavy chain	B
Light chain
Heavy subgroup	IGHV1
Light subgroup
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80	81	82	82A	82B	82C	83	84	85	86	87	88	89	90	91	92	93	94	95	96	97	98	99	100	100A	100B	100C	100D	100E	100F	100G	100H	100I	101	102	103	104	105	106	107	108	109	110	111	112	113
G	S	L	R	L	S	C	A	A	S	G	R	T	F	S	T	A	A	M	G	W	F	R	Q	A	P	G	K	E	R	D	F	V	A	G	I	Y	W	T	V	G	S	T	Y	Y	A	D	S	A	K	G	R	F	T	I	S	R	D	N	A	K	N	T	V	Y	L	Q	M	D	S	L	K	P	E	D	T	A	V	Y	Y	C	A	A	R	R	R	G	F	T	L	A	P	T	R	A	N	E	Y	D	Y	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen species	SYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1	GRTFSTA
CDRH2	YWTVGS
CDRH3	RRRGFTLAPTRANEYDY

Fv Details
Heavy chain	E
Light chain
Heavy subgroup	IGHV1
Light subgroup
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80	81	82	82A	82B	82C	83	84	85	86	87	88	89	90	91	92	93	94	95	96	97	98	99	100	100A	100B	100C	100D	100E	100F	100G	100H	100I	101	102	103	104	105	106	107	108	109	110	111	112	113
G	S	L	R	L	S	C	A	A	S	G	R	T	F	S	T	A	A	M	G	W	F	R	Q	A	P	G	K	E	R	D	F	V	A	G	I	Y	W	T	V	G	S	T	Y	Y	A	D	S	A	K	G	R	F	T	I	S	R	D	N	A	K	N	T	V	Y	L	Q	M	D	S	L	K	P	E	D	T	A	V	Y	Y	C	A	A	R	R	R	G	F	T	L	A	P	T	R	A	N	E	Y	D	Y	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen species	SYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1	GRTFSTA
CDRH2	YWTVGS
CDRH3	RRRGFTLAPTRANEYDY

Fv Details
Heavy chain	A
Light chain
Heavy subgroup	IGHV1
Light subgroup
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80	81	82	82A	82B	82C	83	84	85	86	87	88	89	90	91	92	93	94	95	96	97	98	99	100	100A	100B	100C	100D	100E	100F	100G	100H	100I	101	102	103	104	105	106	107	108	109	110	111	112	113
G	S	L	R	L	S	C	A	A	S	G	R	T	F	S	T	A	A	M	G	W	F	R	Q	A	P	G	K	E	R	D	F	V	A	G	I	Y	W	T	V	G	S	T	Y	Y	A	D	S	A	K	G	R	F	T	I	S	R	D	N	A	K	N	T	V	Y	L	Q	M	D	S	L	K	P	E	D	T	A	V	Y	Y	C	A	A	R	R	R	G	F	T	L	A	P	T	R	A	N	E	Y	D	Y	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen species	SYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1	GRTFSTA
CDRH2	YWTVGS
CDRH3	RRRGFTLAPTRANEYDY

Fv Details
Heavy chain	J
Light chain
Heavy subgroup	IGHV1
Light subgroup
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80	81	82	82A	82B	82C	83	84	85	86	87	88	89	90	91	92	93	94	95	96	97	98	99	100	100A	100B	100C	100D	100E	100F	100G	100H	100I	101	102	103	104	105	106	107	108	109	110	111	112	113
G	S	L	R	L	S	C	A	A	S	G	R	T	F	S	T	A	A	M	G	W	F	R	Q	A	P	G	K	E	R	D	F	V	A	G	I	Y	W	T	V	G	S	T	Y	Y	A	D	S	A	K	G	R	F	T	I	S	R	D	N	A	K	N	T	V	Y	L	Q	M	D	S	L	K	P	E	D	T	A	V	Y	Y	C	A	A	R	R	R	G	F	T	L	A	P	T	R	A	N	E	Y	D	Y	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen species	SYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1	GRTFSTA
CDRH2	YWTVGS
CDRH3	RRRGFTLAPTRANEYDY

Fv Details
Heavy chain	H
Light chain
Heavy subgroup	IGHV1
Light subgroup
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80	81	82	82A	82B	82C	83	84	85	86	87	88	89	90	91	92	93	94	95	96	97	98	99	100	100A	100B	100C	100D	100E	100F	100G	100H	100I	101	102	103	104	105	106	107	108	109	110	111	112	113
G	S	L	R	L	S	C	A	A	S	G	R	T	F	S	T	A	A	M	G	W	F	R	Q	A	P	G	K	E	R	D	F	V	A	G	I	Y	W	T	V	G	S	T	Y	Y	A	D	S	A	K	G	R	F	T	I	S	R	D	N	A	K	N	T	V	Y	L	Q	M	D	S	L	K	P	E	D	T	A	V	Y	Y	C	A	A	R	R	R	G	F	T	L	A	P	T	R	A	N	E	Y	D	Y	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen species	SYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1	GRTFSTA
CDRH2	YWTVGS
CDRH3	RRRGFTLAPTRANEYDY

Fv Details
Heavy chain	C
Light chain
Heavy subgroup	IGHV1
Light subgroup
Species	CHIMERIC HELICOBACTER PYLORI/HELICOBACTER PYLORI(STRAIN G27)
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80	81	82	82A	82B	82C	83	84	85	86	87	88	89	90	91	92	93	94	95	96	97	98	99	100	100A	100B	100C	100D	100E	100F	100G	100H	100I	101	102	103	104	105	106	107	108	109	110	111	112	113
G	S	L	R	L	S	C	A	A	S	G	R	T	F	S	T	A	A	M	G	W	F	R	Q	A	P	G	K	E	R	D	F	V	A	G	I	Y	W	T	V	G	S	T	Y	Y	A	D	S	A	K	G	R	F	T	I	S	R	D	N	A	K	N	T	V	Y	L	Q	M	D	S	L	K	P	E	D	T	A	V	Y	Y	C	A	A	R	R	R	G	F	T	L	A	P	T	R	A	N	E	Y	D	Y	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen species	SYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1	GRTFSTA
CDRH2	YWTVGS
CDRH3	RRRGFTLAPTRANEYDY

Additional links and files for download: see help for more details.

Chothia-numbered structure	Download
IMGT-numbered structure	Download
Non-annotated structure from the PDB	Download
Summary file for this antibody	Download

Schneider, C., Raybould, M.I.J., Deane, C.M. (2022) SAbDab in the Age of Biotherapeutics: Updates including SAbDab-Nano, the Nanobody Structure Tracker. Nucleic Acids Res. 50(D1):D1368-D1372 [link]

SAbDab paper: Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 [link]

Thera-SAbDab paper: Raybould, M.I.J., Marks, C. et al (2019). Nucleic Acids Res. gkz827 [link]

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