SMTL ID : 7d30.1

Structure of sybody MR17-SR31 fusion in complex with the SARS-CoV-2 S Receptor Binding domain (RBD)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC-FUC.1: 8 residues within 4Å: Chain B: N.17, L.42, Y.43, N.44, S.47, F.48, W.110 Ligands: 1PE.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.48, B:W.110, B:L.42 Water bridges: B:N.111, B:N.114, B:N.44, B:N.44

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: V.160, Q.161, Y.262 Chain B: S.45, F.48, S.49, T.50 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.159, A:V.160, A:Y.262 Water bridges: A:L.162 GOL.9: 3 residues within 4Å: Chain A: E.34, N.78 Ligands: ACT.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.78 Water bridges: A:E.34 GOL.32: 4 residues within 4Å: Chain B: S.49, T.50, G.78, Y.182 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.50 GOL.33: 6 residues within 4Å: Chain B: T.50, K.52, Y.54, I.84, A.85, V.107 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.52, B:Y.54, B:I.84 Water bridges: B:T.50 GOL.38: 5 residues within 4Å: Chain A: A.65 Chain B: T.152, G.159, F.160, N.161 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.160, B:N.161, B:N.161

14 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: D.220, K.223 Chain B: Q.213 Ligands: CD.15, ACT.30 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.223 ACT.4: 4 residues within 4Å: Chain A: K.245, P.246, E.247 Ligands: CD.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.245 Salt bridges: A:K.245 ACT.5: 4 residues within 4Å: Chain A: R.230, D.231, N.232, A.233 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.232, A:N.232, A:A.233 ACT.7: 6 residues within 4Å: Chain A: P.32, E.34, N.78, N.81 Ligands: ACT.8, CD.20 No protein-ligand interaction detected (PLIP) ACT.8: 5 residues within 4Å: Chain A: E.34, N.78 Ligands: ACT.7, GOL.9, CD.20 No protein-ligand interaction detected (PLIP) ACT.13: 6 residues within 4Å: Chain A: Y.218, K.223, G.224, R.225, F.226, T.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.224, A:F.226, A:F.226 ACT.14: 5 residues within 4Å: Chain A: H.60 Chain B: Y.25, L.126, F.164 Ligands: BU2.12 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.60 ACT.27: 2 residues within 4Å: Chain B: R.20, A.22 No protein-ligand interaction detected (PLIP) ACT.29: 4 residues within 4Å: Chain B: R.29, Y.70, F.138, S.188 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.138 Salt bridges: B:R.29 ACT.30: 4 residues within 4Å: Chain A: D.220 Chain B: Q.213 Ligands: ACT.3, CD.15 No protein-ligand interaction detected (PLIP) ACT.31: 3 residues within 4Å: Chain B: Y.25, A.26, R.140 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.26 Hydrogen bonds: B:Y.25 Water bridges: B:R.140 Salt bridges: B:R.140 ACT.34: 2 residues within 4Å: Chain B: D.102 Ligands: CD.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.101, B:D.102 ACT.35: 6 residues within 4Å: Chain B: R.131, E.139, R.140, D.141, S.143 Ligands: CD.43 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.141 Hydrogen bonds: B:R.131, B:D.141, B:S.143 Water bridges: B:S.143 ACT.39: 3 residues within 4Å: Chain B: W.27, R.29, R.140 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.29 Water bridges: B:R.29 Salt bridges: B:R.29

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 8 residues within 4Å: Chain A: R.203 Chain B: G.13, N.17, S.40, V.41, L.42 Ligands: NAG-NAG-BMA-MAN-FUC-FUC.1, NAG-NAG-BMA-MAN-FUC-FUC.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.203, A:R.203 Water bridges: B:N.17 1PE.28: 6 residues within 4Å: Chain B: G.55, V.56, K.60, T.67, F.189, L.191 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.60

5 x BU2: 1,3-BUTANEDIOL(Non-covalent)

BU2.10: 6 residues within 4Å: Chain A: A.182, S.183, G.184, F.185, N.235 Ligands: BU2.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.182, A:F.185 BU2.11: 6 residues within 4Å: Chain A: P.186, V.187, W.188, N.232, N.235 Ligands: BU2.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.188 BU2.12: 3 residues within 4Å: Chain A: Y.58, H.60 Ligands: ACT.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.58, A:Y.58 BU2.36: 5 residues within 4Å: Chain A: Y.110 Chain B: T.174, N.175, G.176, Q.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.174, B:Q.180 BU2.37: 4 residues within 4Å: Chain B: F.130, A.149, N.161, Y.163 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.149, B:Y.163 Hydrogen bonds: B:Y.163

17 x CD: CADMIUM ION(Non-covalent)

CD.15: 5 residues within 4Å: Chain A: D.220, K.223 Chain B: Q.213 Ligands: ACT.3, ACT.30 Ligand excluded by PLIP CD.16: 2 residues within 4Å: Chain A: P.92, E.93 Ligand excluded by PLIP CD.17: 1 residues within 4Å: Chain A: M.212 Ligand excluded by PLIP CD.18: 4 residues within 4Å: Chain A: V.102, K.103 Ligands: CD.24, CD.25 Ligand excluded by PLIP CD.19: 2 residues within 4Å: Chain A: E.247 Ligands: ACT.4 Ligand excluded by PLIP CD.20: 3 residues within 4Å: Chain A: N.78 Ligands: ACT.7, ACT.8 Ligand excluded by PLIP CD.21: 2 residues within 4Å: Chain A: D.66 Chain B: T.152 Ligand excluded by PLIP CD.22: 2 residues within 4Å: Chain A: E.50, S.67 Ligand excluded by PLIP CD.23: 2 residues within 4Å: Chain A: G.70, F.72 Ligand excluded by PLIP CD.24: 5 residues within 4Å: Chain A: V.102, D.104, D.113 Ligands: CD.18, CD.25 Ligand excluded by PLIP CD.25: 5 residues within 4Å: Chain A: D.104, D.113 Ligands: CD.18, CD.24, CD.26 Ligand excluded by PLIP CD.26: 5 residues within 4Å: Chain A: D.104, L.108, H.111, D.113 Ligands: CD.25 Ligand excluded by PLIP CD.40: 2 residues within 4Å: Chain B: D.102 Ligands: ACT.34 Ligand excluded by PLIP CD.41: 1 residues within 4Å: Chain B: D.101 Ligand excluded by PLIP CD.42: 1 residues within 4Å: Chain B: E.14 Ligand excluded by PLIP CD.43: 3 residues within 4Å: Chain B: D.141, S.143 Ligands: ACT.35 Ligand excluded by PLIP CD.44: 5 residues within 4Å: Chain A: R.63 Chain B: N.155, G.156, V.157, E.158 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yao, H. et al., A high-affinity RBD-targeting nanobody improves fusion partner's potency against SARS-CoV-2. Plos Pathog. (2021)

Release Date

2021-02-17

Peptides

sybody fusion of MR17-SR31 with a GS linker: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

sybody fusion of MR17-SR31 with a GS linker

Spike protein S1

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