SMTL ID : 7d2z.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-FUC-FUC.1: 8 residues within 4Å: Chain A: Y.99 Chain B: N.17, L.42, Y.43, N.44, S.47, F.48, W.110 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.48, B:W.110, B:L.42 Water bridges: B:A.46, B:N.111, B:N.44, B:N.44 Hydrogen bonds: A:Y.99, A:Y.99

13 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 2 residues within 4Å: Chain A: R.23, S.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.23, A:R.23, A:S.75 FMT.3: 4 residues within 4Å: Chain A: R.76, D.77, N.78, A.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.77, A:N.78, A:N.78, A:A.79 FMT.6: 2 residues within 4Å: Chain A: W.34, N.78 No protein-ligand interaction detected (PLIP) FMT.8: 4 residues within 4Å: Chain B: L.9, A.37, D.38, Y.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.38, B:Y.39 Water bridges: B:S.40 FMT.9: 2 residues within 4Å: Chain B: A.22, N.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.28 FMT.10: 5 residues within 4Å: Chain B: W.27, N.28, R.29, R.140 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.28, B:R.29 FMT.11: 3 residues within 4Å: Chain B: S.49, Y.182 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.49, B:Y.182 FMT.12: 3 residues within 4Å: Chain B: F.164, L.166, Q.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.167 FMT.16: 3 residues within 4Å: Chain B: L.192, H.193, A.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.193, B:A.194 FMT.17: 1 residues within 4Å: Chain B: K.203 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.203 FMT.19: 3 residues within 4Å: Chain B: G.87, Q.88, T.89 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.89 FMT.20: 3 residues within 4Å: Chain B: T.197, V.198, C.199 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.199 Water bridges: B:T.197 FMT.21: 5 residues within 4Å: Chain B: R.77, Y.127, S.168, Y.169 Ligands: ACT.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.77, B:Y.127 Water bridges: B:G.170

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: Q.35, G.36, E.37, S.57, M.103 Chain B: N.62, K.202 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.62, A:Q.35, A:E.37, A:S.57 Water bridges: B:P.201 GOL.13: 8 residues within 4Å: Chain B: T.50, K.52, Y.54, V.81, R.82, I.84, A.85, V.107 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.50, B:K.52, B:Y.54, B:I.84 GOL.14: 6 residues within 4Å: Chain B: S.49, T.50, G.78, V.81, Y.182 Ligands: FMT.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.50 GOL.15: 3 residues within 4Å: Chain B: F.138, R.140 Ligands: FMT.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.138 Water bridges: B:R.29, B:R.29 GOL.18: 7 residues within 4Å: Chain B: P.100, D.102, F.103, T.104, F.138, S.188, F.189 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.102, B:T.104, B:F.189

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

ACT.5: 8 residues within 4Å: Chain A: Q.5, V.6, Y.108 Chain B: S.45, F.48, S.49, T.50, F.51 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.5, A:Y.108, B:F.48 ACT.7: 6 residues within 4Å: Chain B: R.77, K.91, Y.127, L.129, Q.167 Ligands: FMT.21 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.127, B:L.129 Water bridges: B:E.80 Salt bridges: B:R.77, B:K.91

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

SR31 against SARS-CoV-2 RBD, non neutralizing: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SR31 against SARS-CoV-2 RBD, non neutralizing

Spike protein S1

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