SMTL ID : 6yz5.1

H11-D4 complex with SARS-CoV-2 RBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain A: F.9, G.10, N.14, V.38, L.39 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.9, A:V.38, A:L.39 Water bridges: A:F.9, A:N.14, A:N.14

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: N.25, R.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.25, A:R.26 EDO.3: 1 residues within 4Å: Chain A: R.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.26 EDO.4: 5 residues within 4Å: Chain A: R.26, Y.67, F.135, S.185 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.26, A:R.26, A:S.185, A:S.185 EDO.5: 7 residues within 4Å: Chain A: R.17, F.18, A.19, S.20, N.121, Y.122 Ligands: ACT.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.17, A:S.20 Water bridges: A:S.20, A:N.121, A:Y.122 EDO.6: 2 residues within 4Å: Chain A: F.127 Chain B: S.104 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.164, B:L.105 EDO.7: 5 residues within 4Å: Chain A: F.100, T.101, S.185, F.186 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.101, A:F.186 EDO.8: 5 residues within 4Å: Chain A: F.13, N.14, S.44, F.45, W.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.13 Water bridges: A:S.44 EDO.11: 7 residues within 4Å: Chain A: T.47, K.49, Y.51, V.78, I.81, A.82, V.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.49, A:Y.51 Water bridges: A:R.79 EDO.12: 4 residues within 4Å: Chain A: S.46, T.47, A.106, Y.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.46, A:G.75 Water bridges: A:S.46 EDO.13: 3 residues within 4Å: Chain A: P.97, D.98, P.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.98 Water bridges: A:K.95, A:K.95 EDO.14: 2 residues within 4Å: Chain A: E.136, R.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.137 EDO.15: 6 residues within 4Å: Chain A: F.161 Chain B: T.31, A.32, W.53, S.54, V.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.53, B:S.54 Water bridges: B:T.31

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

ACT.9: 4 residues within 4Å: Chain A: R.17, F.18, N.25 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.25 ACT.10: 4 residues within 4Å: Chain A: R.74, Y.166, G.167, Y.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.167 Water bridges: A:R.74 Salt bridges: A:R.74 ACT.16: 4 residues within 4Å: Chain B: Q.39, R.45, Y.95, W.117 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.95 Salt bridges: B:R.45 ACT.17: 3 residues within 4Å: Chain B: G.55, G.56, R.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.55 Water bridges: B:R.72 Salt bridges: B:R.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naismith, J.H., H11-D4 complex with SARS-CoV-2 RBD. To Be Published

Release Date

2020-06-03

Peptides

Spike glycoprotein: A
Nanobody H11-D4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Spike glycoprotein

Nanobody H11-D4

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