Structure Viewer: 9bop

> Structure details

a Broadly-Neutralizing antibody against Ebolavirus Glycoprotein That Can Potentiate the Breadth and Neutralization Potency of Other anti-Glycoprotein antibodies

PDB	9bop
Species	ORYCTOLAGUS CUNICULUS
Method	ELECTRON MICROSCOPY
Resolution	3.0Å
Number of Fvs	5
In complex	True
Light chain type	Kappa
Has constant region	False

> Fv information

This PDB has 5 Fv(s).

Fv Details
Heavy chain	A
Light chain	B
Heavy subgroup	IGHV1
Light subgroup	IGKV1
Species	ORYCTOLAGUS CUNICULUS
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	31A	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	52B	52C	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	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	101	102	103	104	105	106	107	108	109	110	111	112
Q	E	Q	L	V	E	S	G	G	G	L	V	Q	P	E	G	S	L	T	L	T	C	T	A	S	G	F	S	F	S	S	N	C	W	R	C	W	V	R	Q	A	P	G	K	G	L	E	W	I	A	C	V	C	A	G	R	S	G	G	T	T	Y	Y	A	S	W	A	K	G	R	F	T	I	S	K	T	S	S	P	T	V	T	L	Q	M	T	S	L	T	A	A	D	T	A	T	Y	F	C	A	R	A	G	Y	D	D	Y	G	D	A	S	F	F	N	L	W	G	P	G	T	L	V	T	V	S

Light chain

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	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	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	83	84	85	86	87	88	89	90	91	92	93	94	95	95A	95B	95C	95D	96	97	98	99	100	101	102	103	104	105	106	107
A	V	V	L	T	Q	T	A	S	P	V	S	T	P	V	G	G	T	V	T	I	K	C	Q	A	S	Q	N	I	Y	S	N	L	A	W	Y	Q	Q	K	P	G	Q	P	P	K	L	L	I	Y	S	A	S	T	L	A	S	G	V	P	S	R	F	K	G	S	G	S	G	T	E	Y	T	L	T	I	S	D	L	E	C	A	D	A	A	T	Y	Y	C	Q	R	Y	Y	Y	L	S	G	S	A	D	N	T	F	G	G	G	T	E	V	V	V	K

Antigen Details
Antigen chains	S
Antigen type	protein
Antigen name	virion spike glycoprotein gp1
Antigen species	EBOLAVIRUS
Antigen sequence	RSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFT

CDR Sequences (chothia definition)
CDRH1	GFSFSSNC
CDRH2	CAGRSGGT
CDRH3	AGYDDYGDASFFNL
CDRL1	QASQNIYSNLA
CDRL2	SASTLAS
CDRL3	QRYYYLSGSADNT

Orientation Angles (from ABangle)
HL	-58.36°
HC1	74.62°
HC2	116.73°
LC1	119.7°
LC2	85.59°
dc	16.94Å

Fv Details
Heavy chain	M
Light chain	N
Heavy subgroup	IGHV1
Light subgroup	IGKV1
Species	ORYCTOLAGUS CUNICULUS
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	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	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	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	101	102	103	104	105	106	107	108	109	110	111	112
C	Q	S	V	E	E	S	G	G	R	L	V	T	P	G	T	P	L	T	L	T	C	I	V	S	G	F	S	L	S	N	Y	Y	M	S	W	V	R	Q	V	P	G	K	G	L	E	W	I	G	V	I	G	W	S	G	T	S	S	Y	A	S	W	A	K	G	R	F	T	I	S	K	T	A	S	T	T	V	D	L	K	I	T	S	P	T	T	E	D	T	A	T	Y	F	C	A	R	V	L	Y	I	G	G	G	F	N	Y	Y	D	A	F	D	P	W	G	P	G	T	L	V	T	V	S

Light chain

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	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	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	83	84	85	86	87	88	89	90	91	92	93	94	95	95A	95B	95C	95D	96	97	98	99	100	101	102	103	104	105	106	107
D	V	V	M	T	Q	T	P	A	S	V	S	E	P	V	G	G	T	V	T	I	K	C	Q	A	S	Q	S	I	G	S	N	L	A	W	Y	Q	Q	K	P	G	Q	P	P	K	L	L	I	Y	A	A	S	T	L	A	S	G	V	P	S	R	F	K	G	S	G	S	G	T	E	F	T	L	T	I	S	D	L	E	C	A	D	A	A	T	Y	Y	C	Q	C	T	Y	Y	D	S	S	Y	V	Y	N	N	F	G	G	G	T	E	V	V	V	K

Antigen Details
Antigen chains	S,V
Antigen type	protein
Antigen name	virion spike glycoprotein gp1; virion spike glycoprotein gp2
Antigen species	EBOLAVIRUS
Antigen sequence	AIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVDKTLPD/RSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFT

CDR Sequences (chothia definition)
CDRH1	GFSLSNY
CDRH2	GWSGT
CDRH3	VLYIGGGFNYYDAFDP
CDRL1	QASQSIGSNLA
CDRL2	AASTLAS
CDRL3	QCTYYDSSYVYNN

Orientation Angles (from ABangle)
HL	-53.73°
HC1	73.16°
HC2	114.51°
LC1	123.07°
LC2	84.13°
dc	17.18Å

Fv Details
Heavy chain	O
Light chain	P
Heavy subgroup	IGHV1
Light subgroup	IGKV1
Species	ORYCTOLAGUS CUNICULUS
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	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	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	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	101	102	103	104	105	106	107	108	109	110	111	112
C	Q	S	V	E	E	S	G	G	R	L	V	T	P	G	T	P	L	T	L	T	C	I	V	S	G	F	S	L	S	N	Y	Y	M	S	W	V	R	Q	V	P	G	K	G	L	E	W	I	G	V	I	G	W	S	G	T	S	S	Y	A	S	W	A	K	G	R	F	T	I	S	K	T	A	S	T	T	V	D	L	K	I	T	S	P	T	T	E	D	T	A	T	Y	F	C	A	R	V	L	Y	I	G	G	G	F	N	Y	Y	D	A	F	D	P	W	G	P	G	T	L	V	T	V	S

Light chain

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	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	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	83	84	85	86	87	88	89	90	91	92	93	94	95	95A	95B	95C	95D	96	97	98	99	100	101	102	103	104	105	106	107
D	V	V	M	T	Q	T	P	A	S	V	S	E	P	V	G	G	T	V	T	I	K	C	Q	A	S	Q	S	I	G	S	N	L	A	W	Y	Q	Q	K	P	G	Q	P	P	K	L	L	I	Y	A	A	S	T	L	A	S	G	V	P	S	R	F	K	G	S	G	S	G	T	E	F	T	L	T	I	S	D	L	E	C	A	D	A	A	T	Y	Y	C	Q	C	T	Y	Y	D	S	S	Y	V	Y	N	N	F	G	G	G	T	E	V	V	V	K

Antigen Details
Antigen chains	T,W
Antigen type	protein
Antigen name	virion spike glycoprotein gp1; virion spike glycoprotein gp2
Antigen species	EBOLAVIRUS
Antigen sequence	AIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVDKTLPD/RSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFT

CDR Sequences (chothia definition)
CDRH1	GFSLSNY
CDRH2	GWSGT
CDRH3	VLYIGGGFNYYDAFDP
CDRL1	QASQSIGSNLA
CDRL2	AASTLAS
CDRL3	QCTYYDSSYVYNN

Orientation Angles (from ABangle)
HL	-54.15°
HC1	72.57°
HC2	114.56°
LC1	123.65°
LC2	83.42°
dc	17.27Å

Fv Details
Heavy chain	C
Light chain	D
Heavy subgroup	IGHV1
Light subgroup	IGKV1
Species	ORYCTOLAGUS CUNICULUS
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	31A	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	52B	52C	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	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	101	102	103	104	105	106	107	108	109	110	111	112
Q	E	Q	L	V	E	S	G	G	G	L	V	Q	P	E	G	S	L	T	L	T	C	T	A	S	G	F	S	F	S	S	N	C	W	R	C	W	V	R	Q	A	P	G	K	G	L	E	W	I	A	C	V	C	A	G	R	S	G	G	T	T	Y	Y	A	S	W	A	K	G	R	F	T	I	S	K	T	S	S	P	T	V	T	L	Q	M	T	S	L	T	A	A	D	T	A	T	Y	F	C	A	R	A	G	Y	D	D	Y	G	D	A	S	F	F	N	L	W	G	P	G	T	L	V	T	V	S

Light chain

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	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	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	83	84	85	86	87	88	89	90	91	92	93	94	95	95A	95B	95C	95D	96	97	98	99	100	101	102	103	104	105	106	107
A	V	V	L	T	Q	T	A	S	P	V	S	T	P	V	G	G	T	V	T	I	K	C	Q	A	S	Q	N	I	Y	S	N	L	A	W	Y	Q	Q	K	P	G	Q	P	P	K	L	L	I	Y	S	A	S	T	L	A	S	G	V	P	S	R	F	K	G	S	G	S	G	T	E	Y	T	L	T	I	S	D	L	E	C	A	D	A	A	T	Y	Y	C	Q	R	Y	Y	Y	L	S	G	S	A	D	N	T	F	G	G	G	T	E	V	V	V	K

Antigen Details
Antigen chains	T
Antigen type	protein
Antigen name	virion spike glycoprotein gp1
Antigen species	EBOLAVIRUS
Antigen sequence	RSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFT

CDR Sequences (chothia definition)
CDRH1	GFSFSSNC
CDRH2	CAGRSGGT
CDRH3	AGYDDYGDASFFNL
CDRL1	QASQNIYSNLA
CDRL2	SASTLAS
CDRL3	QRYYYLSGSADNT

Orientation Angles (from ABangle)
HL	-58.21°
HC1	74.54°
HC2	116.77°
LC1	119.55°
LC2	85.75°
dc	16.9Å

Fv Details
Heavy chain	E
Light chain	F
Heavy subgroup	IGHV1
Light subgroup	IGKV1
Species	ORYCTOLAGUS CUNICULUS
In complex?	True
scFv?	False
Has constant domain?	False

Numbered Sequences (chothia)

Heavy chain

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	31A	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	52A	52B	52C	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	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	101	102	103	104	105	106	107	108	109	110	111	112
Q	E	Q	L	V	E	S	G	G	G	L	V	Q	P	E	G	S	L	T	L	T	C	T	A	S	G	F	S	F	S	S	N	C	W	R	C	W	V	R	Q	A	P	G	K	G	L	E	W	I	A	C	V	C	A	G	R	S	G	G	T	T	Y	Y	A	S	W	A	K	G	R	F	T	I	S	K	T	S	S	P	T	V	T	L	Q	M	T	S	L	T	A	A	D	T	A	T	Y	F	C	A	R	A	G	Y	D	D	Y	G	D	A	S	F	F	N	L	W	G	P	G	T	L	V	T	V	S

Light chain

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	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	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	83	84	85	86	87	88	89	90	91	92	93	94	95	95A	95B	95C	95D	96	97	98	99	100	101	102	103	104	105	106	107
A	V	V	L	T	Q	T	A	S	P	V	S	T	P	V	G	G	T	V	T	I	K	C	Q	A	S	Q	N	I	Y	S	N	L	A	W	Y	Q	Q	K	P	G	Q	P	P	K	L	L	I	Y	S	A	S	T	L	A	S	G	V	P	S	R	F	K	G	S	G	S	G	T	E	Y	T	L	T	I	S	D	L	E	C	A	D	A	A	T	Y	Y	C	Q	R	Y	Y	Y	L	S	G	S	A	D	N	T	F	G	G	G	T	E	V	V	V	K

Antigen Details
Antigen chains	U
Antigen type	protein
Antigen name	virion spike glycoprotein gp1
Antigen species	EBOLAVIRUS
Antigen sequence	RSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFT

CDR Sequences (chothia definition)
CDRH1	GFSFSSNC
CDRH2	CAGRSGGT
CDRH3	AGYDDYGDASFFNL
CDRL1	QASQNIYSNLA
CDRL2	SASTLAS
CDRL3	QRYYYLSGSADNT

Orientation Angles (from ABangle)
HL	-57.75°
HC1	74.77°
HC2	117.75°
LC1	120.55°
LC2	85.94°
dc	16.89Å

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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