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> Structure details

Crystal Structure of the complex of Wuhan Sars-Cov-2 Rbd (319-541) with P2C5 Nanobody

PDB	8zer
Species	CAMELUS BACTRIANUS
Method	X-RAY DIFFRACTION
Resolution	3.1Å
Number of Fvs	5
In complex	True
Light chain type	NA
Has constant region	False

> Fv information

This PDB has 5 Fv(s).

Fv Details
Heavy chain	A
Light chain
Heavy subgroup	IGHV1
Light subgroup	NA
Species	CAMELUS BACTRIANUS
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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	G	S	V	Q	A	G	G	S	L	R	L	S	C	V	A	S	G	Y	T	Y	C	S	Y	D	M	S	W	Y	R	Q	A	P	G	K	E	R	E	F	V	S	I	I	R	R	D	G	S	T	A	Y	T	D	A	V	K	G	R	F	A	I	S	R	D	N	A	K	N	T	L	Y	L	Q	M	N	S	L	E	P	E	D	T	A	M	Y	Y	C	K	S	W	A	C	S	S	G	E	Y	L	Y	Q	G	D	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains	C
Antigen type	protein
Antigen name	spike protein s1
Antigen species	SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequence	RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFGSHHHHHHHHHH

CDR Sequences (chothia definition)
CDRH1	GYTYCSY
CDRH2	RRDGS
CDRH3	WACSSGEYLYQGD

Fv Details
Heavy chain	D
Light chain
Heavy subgroup	IGHV1
Light subgroup	NA
Species	CAMELUS BACTRIANUS
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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	G	S	V	Q	A	G	G	S	L	R	L	S	C	V	A	S	G	Y	T	Y	C	S	Y	D	M	S	W	Y	R	Q	A	P	G	K	E	R	E	F	V	S	I	I	R	R	D	G	S	T	A	Y	T	D	A	V	K	G	R	F	A	I	S	R	D	N	A	K	N	T	L	Y	L	Q	M	N	S	L	E	P	E	D	T	A	M	Y	Y	C	K	S	W	A	C	S	S	G	E	Y	L	Y	Q	G	D	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains	I
Antigen type	protein
Antigen name	spike protein s1
Antigen species	SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequence	RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFGSHHHHHHHHHH

CDR Sequences (chothia definition)
CDRH1	GYTYCSY
CDRH2	RRDGS
CDRH3	WACSSGEYLYQGD

Fv Details
Heavy chain	F
Light chain
Heavy subgroup	IGHV1
Light subgroup	NA
Species	CAMELUS BACTRIANUS
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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	G	S	V	Q	A	G	G	S	L	R	L	S	C	V	A	S	G	Y	T	Y	C	S	Y	D	M	S	W	Y	R	Q	A	P	G	K	E	R	E	F	V	S	I	I	R	R	D	G	S	T	A	Y	T	D	A	V	K	G	R	F	A	I	S	R	D	N	A	K	N	T	L	Y	L	Q	M	N	S	L	E	P	E	D	T	A	M	Y	Y	C	K	S	W	A	C	S	S	G	E	Y	L	Y	Q	G	D	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains	B,E
Antigen type	protein
Antigen name	spike protein s1
Antigen species	SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequence	RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFGSHHHHHHHHHH/RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFGSHHHHHHHHHH

CDR Sequences (chothia definition)
CDRH1	GYTYCSY
CDRH2	RRDGS
CDRH3	WACSSGEYLYQGD

Fv Details
Heavy chain	H
Light chain
Heavy subgroup	IGHV1
Light subgroup	NA
Species	CAMELUS BACTRIANUS
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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	G	S	V	Q	A	G	G	S	L	R	L	S	C	V	A	S	G	Y	T	Y	C	S	Y	D	M	S	W	Y	R	Q	A	P	G	K	E	R	E	F	V	S	I	I	R	R	D	G	S	T	A	Y	T	D	A	V	K	G	R	F	A	I	S	R	D	N	A	K	N	T	L	Y	L	Q	M	N	S	L	E	P	E	D	T	A	M	Y	Y	C	K	S	W	A	C	S	S	G	E	Y	L	Y	Q	G	D	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains	G
Antigen type	protein
Antigen name	spike protein s1
Antigen species	SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequence	RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFGSHHHHHHHHHH

CDR Sequences (chothia definition)
CDRH1	GYTYCSY
CDRH2	RRDGS
CDRH3	WACSSGEYLYQGD

Fv Details
Heavy chain	J
Light chain
Heavy subgroup	IGHV1
Light subgroup	NA
Species	CAMELUS BACTRIANUS
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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	G	S	V	Q	A	G	G	S	L	R	L	S	C	V	A	S	G	Y	T	Y	C	S	Y	D	M	S	W	Y	R	Q	A	P	G	K	E	R	E	F	V	S	I	I	R	R	D	G	S	T	A	Y	T	D	A	V	K	G	R	F	A	I	S	R	D	N	A	K	N	T	L	Y	L	Q	M	N	S	L	E	P	E	D	T	A	M	Y	Y	C	K	S	W	A	C	S	S	G	E	Y	L	Y	Q	G	D	W	G	Q	G	T	Q	V	T	V	S	S

Antigen Details
Antigen chains	I
Antigen type	protein
Antigen name	spike protein s1
Antigen species	SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequence	RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFGSHHHHHHHHHH

CDR Sequences (chothia definition)
CDRH1	GYTYCSY
CDRH2	RRDGS
CDRH3	WACSSGEYLYQGD

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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