Structure Viewer: 5viy

> Structure details

Bg505 Sosip.664 in complex with Broadly Neutralizing antibodies Bg1 and 8anc195

PDB	5viy
Species	HOMO SAPIENS
Method	ELECTRON MICROSCOPY
Resolution	6.2Å
Number of Fvs	5
In complex	True
Light chain type	Kappa
Has constant region	True

> Fv information

This PDB has 5 Fv(s).

Fv Details
Heavy chain	H
Light chain	G
Heavy subgroup	unknown
Light subgroup	IGKV1
Species	HOMO SAPIENS
In complex?	True
scFv?	False
Has constant domain?	True

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	52A	52B	52C	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	100J	100K	100L	100M	100N	101	102	103	104	105	106	107	108	109	110	111	112	113
A	E	Q	L	V	E	S	G	G	G	L	V	P	P	G	R	S	L	R	L	S	C	S	A	S	G	F	Y	F	P	D	Y	A	M	A	W	V	R	Q	A	P	G	Q	G	L	Q	W	V	G	F	M	R	G	W	A	Y	G	G	S	A	Q	F	A	A	F	A	V	G	K	F	A	I	S	R	D	D	G	R	N	V	V	Y	L	D	V	K	N	P	T	F	E	D	T	G	V	Y	F	C	A	R	E	Q	R	N	K	D	Y	R	Y	G	Q	E	G	F	G	Y	S	Y	G	M	D	V	W	G	R	G	T	T	V	V	V	S	T

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	96	97	98	99	100	101	102	103	104	105	106	107
D	I	H	M	T	Q	S	P	V	S	L	S	A	S	V	G	D	R	V	T	I	T	C	R	A	S	H	F	I	A	N	Y	V	N	W	Y	Q	Q	K	P	G	K	A	P	T	L	L	I	F	E	S	S	T	L	Q	R	G	V	P	S	R	F	S	A	Y	G	D	G	T	E	F	T	L	S	I	N	T	L	Q	P	E	D	F	A	S	Y	I	C	Q	Q	S	H	S	P	P	V	T	F	G	A	G	T	R	V	D	Q	K

Antigen Details
Antigen chains	F
Antigen type	protein
Antigen name	envelope glycoprotein gp160
Antigen species	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequence	AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1	GFYFPDY
CDRH2	RGWAYGGS
CDRH3	EQRNKDYRYGQEGFGYSYGMDV
CDRL1	RASHFIANYVN
CDRL2	ESSTLQR
CDRL3	QQSHSPPVT

Orientation Angles (from ABangle)
HL	-60.66°
HC1	70.74°
HC2	118.05°
LC1	119.8°
LC2	83.49°
dc	17.5Å

Fv Details
Heavy chain	O
Light chain	P
Heavy subgroup	unknown
Light subgroup	IGKV1
Species	HOMO SAPIENS
In complex?	True
scFv?	False
Has constant domain?	True

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	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	71A	72	72A	72B	72C	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	100J	100K	100L	101	102	103	104	105	106	107	108	109	110	111	112	113
Q	I	H	L	V	Q	S	G	T	E	V	K	K	P	G	S	S	V	T	V	S	C	K	A	Y	G	V	N	T	F	G	L	Y	A	V	N	W	V	R	Q	A	P	G	Q	S	L	E	Y	I	G	Q	I	W	R	W	K	S	S	A	S	H	H	F	R	G	R	V	L	I	S	A	V	D	L	T	G	S	S	P	P	I	S	S	L	E	I	K	N	L	T	S	D	D	T	A	V	Y	F	C	T	T	T	S	T	Y	D	R	W	S	G	L	H	H	D	G	V	M	A	F	S	S	W	G	Q	G	T	L	I	S	V	S	A

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	30A	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	96	97	98	99	100	101	102	103	104	105	106	107
D	I	Q	M	T	Q	S	P	S	T	L	S	A	S	T	G	D	T	V	R	I	S	C	R	A	S	Q	S	I	T	G	N	W	V	A	W	Y	Q	Q	R	P	G	K	A	P	R	L	L	I	Y	R	G	A	A	L	L	G	G	V	P	S	R	F	R	G	S	A	A	G	T	D	F	T	L	T	I	G	N	L	Q	A	E	D	F	G	T	F	Y	C	Q	Q	Y	D	T	Y	P	G	T	F	G	Q	G	T	K	V	E	V	K

Antigen Details
Antigen chains	C,E
Antigen type	protein
Antigen name	envelope glycoprotein gp160
Antigen species	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequence	AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD/AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1	GVNTFGLY
CDRH2	WRWK
CDRH3	TSTYDRWSGLHHDGVMAFSS
CDRL1	RASQSITGNWVA
CDRL2	RGAALLG
CDRL3	QQYDTYPGT

Orientation Angles (from ABangle)
HL	-64.36°
HC1	72.38°
HC2	116.35°
LC1	118.68°
LC2	84.45°
dc	15.94Å

Fv Details
Heavy chain	J
Light chain	I
Heavy subgroup	unknown
Light subgroup	IGKV1
Species	HOMO SAPIENS
In complex?	True
scFv?	False
Has constant domain?	True

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	52A	52B	52C	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	100J	100K	100L	100M	100N	101	102	103	104	105	106	107	108	109	110	111	112	113
A	E	Q	L	V	E	S	G	G	G	L	V	P	P	G	R	S	L	R	L	S	C	S	A	S	G	F	Y	F	P	D	Y	A	M	A	W	V	R	Q	A	P	G	Q	G	L	Q	W	V	G	F	M	R	G	W	A	Y	G	G	S	A	Q	F	A	A	F	A	V	G	K	F	A	I	S	R	D	D	G	R	N	V	V	Y	L	D	V	K	N	P	T	F	E	D	T	G	V	Y	F	C	A	R	E	Q	R	N	K	D	Y	R	Y	G	Q	E	G	F	G	Y	S	Y	G	M	D	V	W	G	R	G	T	T	V	V	V	S	T

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	96	97	98	99	100	101	102	103	104	105	106	107
D	I	H	M	T	Q	S	P	V	S	L	S	A	S	V	G	D	R	V	T	I	T	C	R	A	S	H	F	I	A	N	Y	V	N	W	Y	Q	Q	K	P	G	K	A	P	T	L	L	I	F	E	S	S	T	L	Q	R	G	V	P	S	R	F	S	A	Y	G	D	G	T	E	F	T	L	S	I	N	T	L	Q	P	E	D	F	A	S	Y	I	C	Q	Q	S	H	S	P	P	V	T	F	G	A	G	T	R	V	D	Q	K

Antigen Details
Antigen chains	D
Antigen type	protein
Antigen name	envelope glycoprotein gp160
Antigen species	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequence	AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1	GFYFPDY
CDRH2	RGWAYGGS
CDRH3	EQRNKDYRYGQEGFGYSYGMDV
CDRL1	RASHFIANYVN
CDRL2	ESSTLQR
CDRL3	QQSHSPPVT

Orientation Angles (from ABangle)
HL	-61.25°
HC1	69.91°
HC2	118.86°
LC1	120.39°
LC2	84.73°
dc	17.53Å

Fv Details
Heavy chain	M
Light chain	N
Heavy subgroup	unknown
Light subgroup	IGKV1
Species	HOMO SAPIENS
In complex?	True
scFv?	False
Has constant domain?	True

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	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	71A	72	72A	72B	72C	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	100J	100K	100L	101	102	103	104	105	106	107	108	109	110	111	112	113
Q	I	H	L	V	Q	S	G	T	E	V	K	K	P	G	S	S	V	T	V	S	C	K	A	Y	G	V	N	T	F	G	L	Y	A	V	N	W	V	R	Q	A	P	G	Q	S	L	E	Y	I	G	Q	I	W	R	W	K	S	S	A	S	H	H	F	R	G	R	V	L	I	S	A	V	D	L	T	G	S	S	P	P	I	S	S	L	E	I	K	N	L	T	S	D	D	T	A	V	Y	F	C	T	T	T	S	T	Y	D	R	W	S	G	L	H	H	D	G	V	M	A	F	S	S	W	G	Q	G	T	L	I	S	V	S	A

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	30A	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	96	97	98	99	100	101	102	103	104	105	106	107
D	I	Q	M	T	Q	S	P	S	T	L	S	A	S	T	G	D	T	V	R	I	S	C	R	A	S	Q	S	I	T	G	N	W	V	A	W	Y	Q	Q	R	P	G	K	A	P	R	L	L	I	Y	R	G	A	A	L	L	G	G	V	P	S	R	F	R	G	S	A	A	G	T	D	F	T	L	T	I	G	N	L	Q	A	E	D	F	G	T	F	Y	C	Q	Q	Y	D	T	Y	P	G	T	F	G	Q	G	T	K	V	E	V	K

Antigen Details
Antigen chains	A
Antigen type	protein
Antigen name	envelope glycoprotein gp160
Antigen species	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequence	AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

CDR Sequences (chothia definition)
CDRH1	GVNTFGLY
CDRH2	WRWK
CDRH3	TSTYDRWSGLHHDGVMAFSS
CDRL1	RASQSITGNWVA
CDRL2	RGAALLG
CDRL3	QQYDTYPGT

Orientation Angles (from ABangle)
HL	-64.36°
HC1	72.38°
HC2	116.35°
LC1	118.68°
LC2	84.45°
dc	15.94Å

Fv Details
Heavy chain	K
Light chain	L
Heavy subgroup	unknown
Light subgroup	IGKV1
Species	HOMO SAPIENS
In complex?	True
scFv?	False
Has constant domain?	True

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	53	54	55	56	57	58	59	60	61	62	63	64	65	66	67	68	69	70	71	71A	72	72A	72B	72C	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	100J	100K	100L	101	102	103	104	105	106	107	108	109	110	111	112	113
Q	I	H	L	V	Q	S	G	T	E	V	K	K	P	G	S	S	V	T	V	S	C	K	A	Y	G	V	N	T	F	G	L	Y	A	V	N	W	V	R	Q	A	P	G	Q	S	L	E	Y	I	G	Q	I	W	R	W	K	S	S	A	S	H	H	F	R	G	R	V	L	I	S	A	V	D	L	T	G	S	S	P	P	I	S	S	L	E	I	K	N	L	T	S	D	D	T	A	V	Y	F	C	T	T	T	S	T	Y	D	R	W	S	G	L	H	H	D	G	V	M	A	F	S	S	W	G	Q	G	T	L	I	S	V	S	A

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	30A	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	96	97	98	99	100	101	102	103	104	105	106	107
D	I	Q	M	T	Q	S	P	S	T	L	S	A	S	T	G	D	T	V	R	I	S	C	R	A	S	Q	S	I	T	G	N	W	V	A	W	Y	Q	Q	R	P	G	K	A	P	R	L	L	I	Y	R	G	A	A	L	L	G	G	V	P	S	R	F	R	G	S	A	A	G	T	D	F	T	L	T	I	G	N	L	Q	A	E	D	F	G	T	F	Y	C	Q	Q	Y	D	T	Y	P	G	T	F	G	Q	G	T	K	V	E	V	K

Antigen Details
Antigen chains	B
Antigen type	protein
Antigen name	envelope glycoprotein gp160
Antigen species	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequence	AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

CDR Sequences (chothia definition)
CDRH1	GVNTFGLY
CDRH2	WRWK
CDRH3	TSTYDRWSGLHHDGVMAFSS
CDRL1	RASQSITGNWVA
CDRL2	RGAALLG
CDRL3	QQYDTYPGT

Orientation Angles (from ABangle)
HL	-64.36°
HC1	72.38°
HC2	116.35°
LC1	118.68°
LC2	84.45°
dc	15.94Å

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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