SAbDab: The Structural Antibody Database

Crystal Structure of Sars-Cov-2 antibody P2C-1F11 with Rbd

PDB	7cdi
Species	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.96Å
Number of Fvs	1
In complex	True
Light chain type	Kappa
Has constant region	True
Affinity	NA

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> Fv information

This PDB has 1 Fv(s).

> H/L

Fv Details
Heavy chain	H
Light chain	L
Heavy subgroup	IGHV3
Light subgroup	IGKV3
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	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	101	102	103	104	105	106	107	108	109	110	111	112	113
E	V	Q	L	V	E	S	G	G	G	L	V	Q	P	G	G	S	L	R	L	S	C	A	A	S	G	I	T	V	S	S	N	Y	M	N	W	V	R	Q	A	P	G	K	G	L	E	W	V	S	L	I	Y	S	G	G	S	T	Y	Y	A	D	S	V	K	G	R	F	T	I	S	R	D	N	S	K	N	T	L	Y	L	Q	M	N	S	L	R	A	E	D	T	A	V	Y	H	C	A	R	D	L	V	V	Y	G	M	D	V	W	G	Q	G	T	T	V	T	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	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	96	97	98	99	100	101	102	103	104	105	106	107
E	I	V	L	T	Q	S	P	G	T	L	S	L	S	P	G	E	R	A	T	L	S	C	R	A	S	Q	S	V	S	S	S	Y	L	A	W	Y	Q	Q	K	P	G	Q	A	P	R	L	L	I	Y	G	A	S	S	R	A	T	G	I	P	D	R	F	S	G	S	G	S	G	T	D	F	T	L	T	I	S	R	L	E	P	E	D	F	A	V	Y	Y	C	Q	Q	Y	G	S	S	P	T	F	G	Q	G	T	K	L	E	I	K

Antigen Details
Antigen chains	E
Antigen type	protein
Antigen name	spike protein s1
Antigen species	SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequence	RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKHHHHHH

CDR Sequences (chothia definition)
CDRH1	GITVSSN
CDRH2	YSGGS
CDRH3	DLVVYGMDV
CDRL1	RASQSVSSSYLA
CDRL2	GASSRAT
CDRL3	QQYGSSPT

Orientation Angles (from ABangle)
HL	-59.97°
HC1	71.4°
HC2	119.6°
LC1	120.9°
LC2	82.22°
dc	16.38Å

> Occurences in auxilliary databases

Occurences of this structure in other OPIG databases.

> CoVAbDab entry

Ab_or_Nb	Ab
Binds_to	SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Beta;SARS-CoV2_Gamma;SARS-CoV2_Delta;SARS-CoV2_Omicron-BA1 (weak);SARS-CoV2_Omicron-BA2 (weak)
Does_not_bind_to	None
Neutralising_vs	SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Beta;SARS-CoV2_Gamma;SARS-CoV2_Delta;SARS-CoV2_Omicron-BA1 (weak);SARS-CoV2_Omicron-BA2 (weak)
Not_Neutralising_vs	None
Protein_and_Epitope	S; RBD
Origin	ND
VH_or_VHH	EVQLVESGGGLVQPGGSLRLSCAASGITVSSNYMNWVRQAPGKGLEWVSLIYSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYHCARDLVVYGMDVWGQGTTVTVSS
VL	EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPTFGQGTKLEIK
Heavy_V_Gene	IGHV3-11 (Human)
Heavy_J_Gene	IGHJ5 (Human)
Light_V_Gene	IGKV1-9 (Human)
Light_J_Gene	IGKJ4 (Human)
CDRH3	ARDLVVYGMDV
CDRL3	QQYGSSPT
Structures	http://www.rcsb.org/structure/7CDI; https://www.rcsb.org/structure/7E8M
ABB_Homology_Model	None
Sources	PDB (http://www.rcsb.org/structure/7CDI); Lihong Liu et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.14.472719v3); Sho Iketani et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.07.479306v1)
Date_Added	Nov 22, 2020
Last_Updated	Mar 4, 2022
Update_Description	27th May '21: Added extra structure (7e8m). 28th Dec '21: Added variant neutralisation data. 4th Mar '22: Added Omicron-BA2 data
Notes_Following_Up	Awaiting publication for full reference and neutralisation data (X. Wang et al.). Therapeutic antibody Amubarvimab. Also known as Brii-196.

TheraSAbDab	link

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Chothia-numbered structure	Download
IMGT-numbered structure	Download
Non-annotated structure from the PDB	Download
Summary file for this antibody	Download

Structure Viewer: 7cdi