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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This PDB has 1 Fv(s).
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 |
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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 |
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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 of this structure in other OPIG databases.
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 |
SAbDab papers
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]
Dunbar, J., Krawczyk, K. et al. (2014) SAbDab: the Structural Antibody Database. Nucleic Acids Res. 42(D1):D1140-D1146 [link]
Thera-SAbDab paper
Raybould, M.I.J., Marks, C. et al (2020) Thera-SAbDab: the Therapeutic Structural Antibody Database. Nucleic Acids Res. 48(D1):D383-D388. [link]