Structure Viewer: 7zlk

> Structure details

amc009 Sosipv5.2 in complex with Fabs acs101 and acs124

PDB	7zlk
Species	HOMO SAPIENS
Method	ELECTRON MICROSCOPY
Resolution	0Å
Number of Fvs	5
In complex	True
Light chain type	Lambda,Kappa
Has constant region	False

> Fv information

This PDB has 5 Fv(s).

Fv Details
Heavy chain	H
Light chain	L
Heavy subgroup	IGHV4
Light subgroup	IGKV2
Species	HOMO SAPIENS
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
Q	V	Q	L	Q	Q	W	G	G	G	L	L	K	P	S	Q	T	L	S	L	T	C	A	V	Y	R	W	T	F	N	D	H	Y	W	S	W	V	R	Q	S	P	G	K	G	L	E	W	I	G	E	I	S	W	G	G	A	T	N	Y	N	P	S	L	K	S	R	V	T	M	S	V	D	T	S	M	S	H	V	S	L	K	M	T	S	V	T	A	A	D	T	G	V	Y	Y	C	V	R	V	G	P	G	P	H	M	A	A	L	D	Y	W	G	H	G	S	R	V	L	V	S	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	30A	30B	30C	30D	30E	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	V	M	T	Q	T	P	L	S	S	P	V	T	L	G	Q	P	A	S	I	S	C	G	S	S	Q	S	L	V	H	S	D	G	N	T	Y	L	S	W	L	Q	Q	R	P	G	Q	P	P	R	L	L	I	Y	K	I	S	N	R	I	S	G	L	P	D	R	F	S	G	S	G	A	E	T	N	F	T	L	K	I	S	R	V	E	A	E	D	V	G	L	Y	Y	C	V	Q	G	T	Q	F	P	W	T	S	G	Q	G	T	K	V	E	I	K

Antigen Details
Antigen chains	D
Antigen type	protein
Antigen name	amc009 sosipv5.2 envelope glycoprotein gp120
Antigen species	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequence	ARADKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVRNVWATHCCVPTDPNPQEVVLENVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDYVGNATNASTTNATGGIGGTVERGEIKNCSFNITTSIRDKVQKEYALFYKLDIVPIDNDNTNNSYRLINCNTSVIKQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEKEVVIRSQNFTNNAKVIIVQLNESVVINCTRPNNNTRKSIHIAPGRWFYTTGAIIGDIRQAHCNISRVKWNNTLKQIATKLREQFKNKTIAFNQSSGGDPEIVMHSFNCGGEFFYCNTTQLFNSTWNDTEVSNYNDITHITLPCRIKQIINMWQKVGKAMYAPPIRGQIRCSSNITGLLLTRDGGSNENKTSETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTKCKRRVVQ

CDR Sequences (chothia definition)
CDRH1	RWTFNDH
CDRH2	SWGGA
CDRH3	VGPGPHMAALDY
CDRL1	GSSQSLVHSDGNTYLS
CDRL2	KISNRIS
CDRL3	VQGTQFPWT

Orientation Angles (from ABangle)
HL	-60.19°
HC1	73.49°
HC2	119.45°
LC1	120.16°
LC2	81.09°
dc	15.99Å

Fv Details
Heavy chain	M
Light chain	N
Heavy subgroup	IGHV4
Light subgroup	IGLV3
Species	HOMO SAPIENS
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
Q	V	Q	L	Q	E	S	G	P	G	L	V	K	P	S	E	A	L	S	L	T	C	S	V	S	G	V	A	I	S	R	H	Y	W	N	W	I	R	Q	P	P	G	K	G	L	E	W	I	G	Y	I	F	F	N	G	N	T	N	Y	S	P	S	L	K	S	R	V	T	I	S	V	D	T	S	K	N	E	F	S	L	T	L	R	S	V	T	A	A	D	T	A	V	Y	Y	C	A	R	E	K	S	V	V	E	P	D	N	M	V	R	W	F	D	P	W	G	Q	G	T	L	V	T	V	S	S

Light chain

1	2	3	4	5	6	7	8	9	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	96	97	98	99	100	101	102	103	104	105	106	107
S	Y	E	L	T	Q	P	P	S	V	S	V	A	P	G	K	T	A	R	I	T	C	G	G	N	N	I	G	S	K	S	V	H	W	Y	Q	Q	K	P	G	Q	A	P	V	L	V	I	Y	Y	D	S	D	R	P	S	G	I	P	E	R	F	S	G	S	K	S	G	N	T	A	T	L	T	I	S	R	V	E	A	G	D	E	A	D	Y	Y	C	Q	V	W	D	S	S	R	D	H	C	V	F	G	I	G	T	K	V	T	V	L

Antigen Details
Antigen chains	F
Antigen type	protein
Antigen name	amc009 sosipv5.2 envelope glycoprotein gp41
Antigen species	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequence	AVGAIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAPECQQHMLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTAVPWNNSWSNRSLDMIWNNMTWIEWEREIDNYTGLIYNLLEESQNQQEKNEQELLELD

CDR Sequences (chothia definition)
CDRH1	GVAISRH
CDRH2	FFNGN
CDRH3	EKSVVEPDNMVRWFDP
CDRL1	GGNNIGSKSVH
CDRL2	YDSDRPS
CDRL3	QVWDSSRDHCV

Orientation Angles (from ABangle)
HL	-55.61°
HC1	73.48°
HC2	120.11°
LC1	121.45°
LC2	85.44°
dc	16.59Å

Fv Details
Heavy chain	O
Light chain	P
Heavy subgroup	IGHV4
Light subgroup	IGKV2
Species	HOMO SAPIENS
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
Q	V	Q	L	Q	Q	W	G	G	G	L	L	K	P	S	Q	T	L	S	L	T	C	A	V	Y	R	W	T	F	N	D	H	Y	W	S	W	V	R	Q	S	P	G	K	G	L	E	W	I	G	E	I	S	W	G	G	A	T	N	Y	N	P	S	L	K	S	R	V	T	M	S	V	D	T	S	M	S	H	V	S	L	K	M	T	S	V	T	A	A	D	T	G	V	Y	Y	C	V	R	V	G	P	G	P	H	M	A	A	L	D	Y	W	G	H	G	S	R	V	L	V	S	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	30A	30B	30C	30D	30E	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	V	M	T	Q	T	P	L	S	S	P	V	T	L	G	Q	P	A	S	I	S	C	G	S	S	Q	S	L	V	H	S	D	G	N	T	Y	L	S	W	L	Q	Q	R	P	G	Q	P	P	R	L	L	I	Y	K	I	S	N	R	I	S	G	L	P	D	R	F	S	G	S	G	A	E	T	N	F	T	L	K	I	S	R	V	E	A	E	D	V	G	L	Y	Y	C	V	Q	G	T	Q	F	P	W	T	S	G	Q	G	T	K	V	E	I	K

Antigen Details
Antigen chains	A
Antigen type	protein
Antigen name	amc009 sosipv5.2 envelope glycoprotein gp120
Antigen species	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequence	ARADKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVRNVWATHCCVPTDPNPQEVVLENVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDYVGNATNASTTNATGGIGGTVERGEIKNCSFNITTSIRDKVQKEYALFYKLDIVPIDNDNTNNSYRLINCNTSVIKQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEKEVVIRSQNFTNNAKVIIVQLNESVVINCTRPNNNTRKSIHIAPGRWFYTTGAIIGDIRQAHCNISRVKWNNTLKQIATKLREQFKNKTIAFNQSSGGDPEIVMHSFNCGGEFFYCNTTQLFNSTWNDTEVSNYNDITHITLPCRIKQIINMWQKVGKAMYAPPIRGQIRCSSNITGLLLTRDGGSNENKTSETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTKCKRRVVQ

CDR Sequences (chothia definition)
CDRH1	RWTFNDH
CDRH2	SWGGA
CDRH3	VGPGPHMAALDY
CDRL1	GSSQSLVHSDGNTYLS
CDRL2	KISNRIS
CDRL3	VQGTQFPWT

Orientation Angles (from ABangle)
HL	-61.09°
HC1	76.18°
HC2	119.79°
LC1	118.82°
LC2	81.08°
dc	15.59Å

Fv Details
Heavy chain	Q
Light chain	R
Heavy subgroup	IGHV4
Light subgroup	IGKV2
Species	HOMO SAPIENS
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
Q	V	Q	L	Q	Q	W	G	G	G	L	L	K	P	S	Q	T	L	S	L	T	C	A	V	Y	R	W	T	F	N	D	H	Y	W	S	W	V	R	Q	S	P	G	K	G	L	E	W	I	G	E	I	S	W	G	G	A	T	N	Y	N	P	S	L	K	S	R	V	T	M	S	V	D	T	S	M	S	H	V	S	L	K	M	T	S	V	T	A	A	D	T	G	V	Y	Y	C	V	R	V	G	P	G	P	H	M	A	A	L	D	Y	W	G	H	G	S	R	V	L	V	S	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	30A	30B	30C	30D	30E	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	V	M	T	Q	T	P	L	S	S	P	V	T	L	G	Q	P	A	S	I	S	C	G	S	S	Q	S	L	V	H	S	D	G	N	T	Y	L	S	W	L	Q	Q	R	P	G	Q	P	P	R	L	L	I	Y	K	I	S	N	R	I	S	G	L	P	D	R	F	S	G	S	G	A	E	T	N	F	T	L	K	I	S	R	V	E	A	E	D	V	G	L	Y	Y	C	V	Q	G	T	Q	F	P	W	T	S	G	Q	G	T	K	V	E	I	K

Antigen Details
Antigen chains	C
Antigen type	protein
Antigen name	amc009 sosipv5.2 envelope glycoprotein gp120
Antigen species	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequence	ARADKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVRNVWATHCCVPTDPNPQEVVLENVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDYVGNATNASTTNATGGIGGTVERGEIKNCSFNITTSIRDKVQKEYALFYKLDIVPIDNDNTNNSYRLINCNTSVIKQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEKEVVIRSQNFTNNAKVIIVQLNESVVINCTRPNNNTRKSIHIAPGRWFYTTGAIIGDIRQAHCNISRVKWNNTLKQIATKLREQFKNKTIAFNQSSGGDPEIVMHSFNCGGEFFYCNTTQLFNSTWNDTEVSNYNDITHITLPCRIKQIINMWQKVGKAMYAPPIRGQIRCSSNITGLLLTRDGGSNENKTSETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTKCKRRVVQ

CDR Sequences (chothia definition)
CDRH1	RWTFNDH
CDRH2	SWGGA
CDRH3	VGPGPHMAALDY
CDRL1	GSSQSLVHSDGNTYLS
CDRL2	KISNRIS
CDRL3	VQGTQFPWT

Orientation Angles (from ABangle)
HL	-61.68°
HC1	73.99°
HC2	118.78°
LC1	120.27°
LC2	81.2°
dc	16.01Å

Fv Details
Heavy chain	S
Light chain	T
Heavy subgroup	IGHV4
Light subgroup	IGLV3
Species	HOMO SAPIENS
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
Q	V	Q	L	Q	E	S	G	P	G	L	V	K	P	S	E	A	L	S	L	T	C	S	V	S	G	V	A	I	S	R	H	Y	W	N	W	I	R	Q	P	P	G	K	G	L	E	W	I	G	Y	I	F	F	N	G	N	T	N	Y	S	P	S	L	K	S	R	V	T	I	S	V	D	T	S	K	N	E	F	S	L	T	L	R	S	V	T	A	A	D	T	A	V	Y	Y	C	A	R	E	K	S	V	V	E	P	D	N	M	V	R	W	F	D	P	W	G	Q	G	T	L	V	T	V	S	S

Light chain

1	2	3	4	5	6	7	8	9	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	96	97	98	99	100	101	102	103	104	105	106	107
S	Y	E	L	T	Q	P	P	S	V	S	V	A	P	G	K	T	A	R	I	T	C	G	G	N	N	I	G	S	K	S	V	H	W	Y	Q	Q	K	P	G	Q	A	P	V	L	V	I	Y	Y	D	S	D	R	P	S	G	I	P	E	R	F	S	G	S	K	S	G	N	T	A	T	L	T	I	S	R	V	E	A	G	D	E	A	D	Y	Y	C	Q	V	W	D	S	S	R	D	H	C	V	F	G	I	G	T	K	V	T	V	L

Antigen Details
Antigen chains	E,B
Antigen type	protein
Antigen name	amc009 sosipv5.2 envelope glycoprotein gp41
Antigen species	HUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequence	AVGAIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAPECQQHMLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTAVPWNNSWSNRSLDMIWNNMTWIEWEREIDNYTGLIYNLLEESQNQQEKNEQELLELD/AVGAIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAPECQQHMLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTAVPWNNSWSNRSLDMIWNNMTWIEWEREIDNYTGLIYNLLEESQNQQEKNEQELLELD

CDR Sequences (chothia definition)
CDRH1	GVAISRH
CDRH2	FFNGN
CDRH3	EKSVVEPDNMVRWFDP
CDRL1	GGNNIGSKSVH
CDRL2	YDSDRPS
CDRL3	QVWDSSRDHCV

Orientation Angles (from ABangle)
HL	-54.25°
HC1	73.09°
HC2	118.91°
LC1	121.21°
LC2	84.93°
dc	16.54Å

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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