SMTL ID : 7zxu.1

SARS-CoV-2 Omicron BA.4/5 RBD in complex with Beta-27 Fab and C1 nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: F.21, A.22, S.23, N.124, Y.125 Ligands: IPA.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.23 Water bridges: A:S.23, A:S.23, A:S.23, A:N.122, A:N.124 GOL.2: 8 residues within 4Å: Chain A: D.102, F.103, T.104, G.105, F.138, S.188, F.189 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.102, A:T.104, A:F.189, A:F.189 GOL.7: 5 residues within 4Å: Chain A: R.29, Y.70, F.138, S.188 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.29, A:R.29, A:S.188, A:S.188 GOL.9: 3 residues within 4Å: Chain B: R.45, P.108, W.114 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.108, B:W.114 GOL.10: 5 residues within 4Å: Chain A: Y.182 Chain B: E.46, T.106, W.107, P.108 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.46, B:T.106, B:T.106, A:Y.182 Water bridges: B:E.46 GOL.11: 8 residues within 4Å: Chain C: Y.149, E.152, P.153, V.154, F.170, P.171, A.172, L.182 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.154, C:V.154, C:A.172 Water bridges: C:E.152, C:E.152 GOL.12: 3 residues within 4Å: Chain A: Y.163 Chain C: Y.102 Chain D: Y.50 1 PLIP interactions: 1 interactions with chain D Water bridges: D:T.57 GOL.13: 4 residues within 4Å: Chain C: K.121, G.122, P.123, S.124 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.121, C:K.121 Water bridges: C:G.122 GOL.15: 6 residues within 4Å: Chain C: Y.59, K.64, G.65, R.66, F.67, T.68 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.65 GOL.17: 6 residues within 4Å: Chain C: G.42, K.43 Chain D: G.9, Y.88, G.100, G.101 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.9, D:K.103, C:K.43

6 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 4 residues within 4Å: Chain A: P.11, R.31, I.32, S.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.33 IPA.4: 3 residues within 4Å: Chain A: R.20, L.115, K.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.118 Water bridges: A:R.20, A:K.118 IPA.6: 3 residues within 4Å: Chain A: R.20, N.28 Ligands: GOL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.28 IPA.8: 1 residues within 4Å: Chain A: D.101 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.101 Hydrogen bonds: A:D.101 IPA.14: 3 residues within 4Å: Chain C: H.72, D.73, S.74 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:D.73 Hydrogen bonds: C:D.73, C:S.74, C:S.74 Water bridges: C:D.73 IPA.18: 4 residues within 4Å: Chain D: S.14, K.107, R.108, T.109 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:T.109 Hydrogen bonds: D:S.14

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

NAG.5: 1 residues within 4Å: Chain A: N.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.17

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.16: 12 residues within 4Å: Chain A: R.77, N.91, Y.127 Chain C: L.50, Y.52, D.98, V.100, V.101 Chain D: S.32, S.33, Y.92, P.96 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: A:R.77, A:R.77, D:S.32, C:Y.52 Water bridges: A:N.91, A:N.91, D:S.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tuekprakhon, A. et al., Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum. Cell (2022)

Release Date

2022-06-29

Peptides

Spike protein S1: A
Nanobody C1: B
Beta-27 heavy chain: C
Beta-27 light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
A

C
H

D
L

Spike protein S1

Nanobody C1

Beta-27 heavy chain

Beta-27 light chain

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