Structure Viewer: 3q6f

> Structure details

Crystal Structure of Fab of Human Mab 2909 Specific For Quaternary Neutralizing Epitope of Hiv-1 Gp120

PDB	3q6f
Species	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	3.192Å
Number of Fvs	6
In complex	True
Light chain type	Lambda
Has constant region	True

> Fv information

This PDB has 6 Fv(s).

Fv Details
Heavy chain	H
Light chain	G
Heavy subgroup	IGHV3
Light subgroup	IGLV3
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	N	V	V	Q	P	G	G	S	L	R	L	S	C	T	A	S	G	F	S	F	D	D	S	T	M	H	W	V	R	Q	A	P	G	K	G	L	Q	W	V	S	L	I	S	W	N	G	G	R	T	Y	Y	A	D	S	V	K	G	R	F	T	I	S	R	D	N	S	K	N	S	L	Y	L	Q	M	N	S	L	K	T	E	D	T	A	F	Y	F	C	A	K	D	K	G	D	S	D	Y	D	Y	N	L	G	Y	S	Y	F	Y	Y	M	D	G	W	G	K	G	T	T	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	V	L	T	Q	P	P	S	V	S	V	A	P	G	K	T	A	R	I	T	C	G	G	N	N	I	A	N	K	N	V	H	W	Y	Q	Q	K	P	G	Q	A	P	V	L	V	I	Y	Y	D	D	D	R	P	S	G	I	P	D	R	F	S	G	S	N	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	N	S	D	H	V	V	F	G	G	G	T	Q	L	T	V	L

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

CDR Sequences (chothia definition)
CDRH1	GFSFDDS
CDRH2	SWNGGR
CDRH3	DKGDSDYDYNLGYSYFYYMDG
CDRL1	GGNNIANKNVH
CDRL2	YDDDRPS
CDRL3	QVWDSNSDHVV

Orientation Angles (from ABangle)
HL	-62.45°
HC1	70.95°
HC2	119.54°
LC1	119.02°
LC2	80.48°
dc	16.51Å

Fv Details
Heavy chain	F
Light chain	E
Heavy subgroup	IGHV3
Light subgroup	IGLV3
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	N	V	V	Q	P	G	G	S	L	R	L	S	C	T	A	S	G	F	S	F	D	D	S	T	M	H	W	V	R	Q	A	P	G	K	G	L	Q	W	V	S	L	I	S	W	N	G	G	R	T	Y	Y	A	D	S	V	K	G	R	F	T	I	S	R	D	N	S	K	N	S	L	Y	L	Q	M	N	S	L	K	T	E	D	T	A	F	Y	F	C	A	K	D	K	G	D	S	D	Y	D	Y	N	L	G	Y	S	Y	F	Y	Y	M	D	G	W	G	K	G	T	T	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	V	L	T	Q	P	P	S	V	S	V	A	P	G	K	T	A	R	I	T	C	G	G	N	N	I	A	N	K	N	V	H	W	Y	Q	Q	K	P	G	Q	A	P	V	L	V	I	Y	Y	D	D	D	R	P	S	G	I	P	D	R	F	S	G	S	N	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	N	S	D	H	V	V	F	G	G	G	T	Q	L	T	V	L

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

CDR Sequences (chothia definition)
CDRH1	GFSFDDS
CDRH2	SWNGGR
CDRH3	DKGDSDYDYNLGYSYFYYMDG
CDRL1	GGNNIANKNVH
CDRL2	YDDDRPS
CDRL3	QVWDSNSDHVV

Orientation Angles (from ABangle)
HL	-63.31°
HC1	71.37°
HC2	119.86°
LC1	118.69°
LC2	78.22°
dc	16.46Å

Fv Details
Heavy chain	D
Light chain	C
Heavy subgroup	IGHV3
Light subgroup	IGLV3
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	N	V	V	Q	P	G	G	S	L	R	L	S	C	T	A	S	G	F	S	F	D	D	S	T	M	H	W	V	R	Q	A	P	G	K	G	L	Q	W	V	S	L	I	S	W	N	G	G	R	T	Y	Y	A	D	S	V	K	G	R	F	T	I	S	R	D	N	S	K	N	S	L	Y	L	Q	M	N	S	L	K	T	E	D	T	A	F	Y	F	C	A	K	D	K	G	D	S	D	Y	D	Y	N	L	G	Y	S	Y	F	Y	Y	M	D	G	W	G	K	G	T	T	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	V	L	T	Q	P	P	S	V	S	V	A	P	G	K	T	A	R	I	T	C	G	G	N	N	I	A	N	K	N	V	H	W	Y	Q	Q	K	P	G	Q	A	P	V	L	V	I	Y	Y	D	D	D	R	P	S	G	I	P	D	R	F	S	G	S	N	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	N	S	D	H	V	V	F	G	G	G	T	Q	L	T	V	L

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

CDR Sequences (chothia definition)
CDRH1	GFSFDDS
CDRH2	SWNGGR
CDRH3	DKGDSDYDYNLGYSYFYYMDG
CDRL1	GGNNIANKNVH
CDRL2	YDDDRPS
CDRL3	QVWDSNSDHVV

Orientation Angles (from ABangle)
HL	-62.05°
HC1	71.18°
HC2	120.06°
LC1	118.89°
LC2	80.03°
dc	16.6Å

Fv Details
Heavy chain	B
Light chain	A
Heavy subgroup	IGHV3
Light subgroup	IGLV3
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	N	V	V	Q	P	G	G	S	L	R	L	S	C	T	A	S	G	F	S	F	D	D	S	T	M	H	W	V	R	Q	A	P	G	K	G	L	Q	W	V	S	L	I	S	W	N	G	G	R	T	Y	Y	A	D	S	V	K	G	R	F	T	I	S	R	D	N	S	K	N	S	L	Y	L	Q	M	N	S	L	K	T	E	D	T	A	F	Y	F	C	A	K	D	K	G	D	S	D	Y	D	Y	N	L	G	Y	S	Y	F	Y	Y	M	D	G	W	G	K	G	T	T	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	V	L	T	Q	P	P	S	V	S	V	A	P	G	K	T	A	R	I	T	C	G	G	N	N	I	A	N	K	N	V	H	W	Y	Q	Q	K	P	G	Q	A	P	V	L	V	I	Y	Y	D	D	D	R	P	S	G	I	P	D	R	F	S	G	S	N	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	N	S	D	H	V	V	F	G	G	G	T	Q	L	T	V	L

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

CDR Sequences (chothia definition)
CDRH1	GFSFDDS
CDRH2	SWNGGR
CDRH3	DKGDSDYDYNLGYSYFYYMDG
CDRL1	GGNNIANKNVH
CDRL2	YDDDRPS
CDRL3	QVWDSNSDHVV

Orientation Angles (from ABangle)
HL	-61.68°
HC1	71.06°
HC2	120.29°
LC1	119.75°
LC2	79.93°
dc	16.47Å

Fv Details
Heavy chain	J
Light chain	I
Heavy subgroup	IGHV3
Light subgroup	IGLV3
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	N	V	V	Q	P	G	G	S	L	R	L	S	C	T	A	S	G	F	S	F	D	D	S	T	M	H	W	V	R	Q	A	P	G	K	G	L	Q	W	V	S	L	I	S	W	N	G	G	R	T	Y	Y	A	D	S	V	K	G	R	F	T	I	S	R	D	N	S	K	N	S	L	Y	L	Q	M	N	S	L	K	T	E	D	T	A	F	Y	F	C	A	K	D	K	G	D	S	D	Y	D	Y	N	L	G	Y	S	Y	F	Y	Y	M	D	G	W	G	K	G	T	T	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	V	L	T	Q	P	P	S	V	S	V	A	P	G	K	T	A	R	I	T	C	G	G	N	N	I	A	N	K	N	V	H	W	Y	Q	Q	K	P	G	Q	A	P	V	L	V	I	Y	Y	D	D	D	R	P	S	G	I	P	D	R	F	S	G	S	N	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	N	S	D	H	V	V	F	G	G	G	T	Q	L	T	V	L

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

CDR Sequences (chothia definition)
CDRH1	GFSFDDS
CDRH2	SWNGGR
CDRH3	DKGDSDYDYNLGYSYFYYMDG
CDRL1	GGNNIANKNVH
CDRL2	YDDDRPS
CDRL3	QVWDSNSDHVV

Orientation Angles (from ABangle)
HL	-62.2°
HC1	70.48°
HC2	119.62°
LC1	119.43°
LC2	80.48°
dc	16.48Å

Fv Details
Heavy chain	L
Light chain	K
Heavy subgroup	IGHV3
Light subgroup	IGLV3
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	N	V	V	Q	P	G	G	S	L	R	L	S	C	T	A	S	G	F	S	F	D	D	S	T	M	H	W	V	R	Q	A	P	G	K	G	L	Q	W	V	S	L	I	S	W	N	G	G	R	T	Y	Y	A	D	S	V	K	G	R	F	T	I	S	R	D	N	S	K	N	S	L	Y	L	Q	M	N	S	L	K	T	E	D	T	A	F	Y	F	C	A	K	D	K	G	D	S	D	Y	D	Y	N	L	G	Y	S	Y	F	Y	Y	M	D	G	W	G	K	G	T	T	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	V	L	T	Q	P	P	S	V	S	V	A	P	G	K	T	A	R	I	T	C	G	G	N	N	I	A	N	K	N	V	H	W	Y	Q	Q	K	P	G	Q	A	P	V	L	V	I	Y	Y	D	D	D	R	P	S	G	I	P	D	R	F	S	G	S	N	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	N	S	D	H	V	V	F	G	G	G	T	Q	L	T	V	L

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

CDR Sequences (chothia definition)
CDRH1	GFSFDDS
CDRH2	SWNGGR
CDRH3	DKGDSDYDYNLGYSYFYYMDG
CDRL1	GGNNIANKNVH
CDRL2	YDDDRPS
CDRL3	QVWDSNSDHVV

Orientation Angles (from ABangle)
HL	-62.52°
HC1	70.83°
HC2	119.87°
LC1	118.54°
LC2	80.17°
dc	16.56Å

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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