SMTL ID : 8bh5.1

SARS-CoV-2 BA.2.12.1 RBD in complex with Beta-27 Fab and C1 nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain C: F.12, D.13, N.17 Ligands: GOL.11 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.12 Hydrogen bonds: C:D.13

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: F.170, P.171, V.173, S.181, L.182, S.183 Chain B: Q.160, S.162, S.176, S.177, T.178 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.160, B:S.162, B:T.178, A:F.170, A:S.183 GOL.3: 4 residues within 4Å: Chain A: R.71, H.72, D.73, S.74 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.72, A:D.73, A:D.73, A:S.74, A:S.74 GOL.4: 3 residues within 4Å: Chain A: L.11, S.119, T.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.120, A:T.120 GOL.5: 6 residues within 4Å: Chain A: H.168, T.169 Chain B: T.164, E.165, Q.166, D.167 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.168, A:T.169, A:T.169, B:Q.166, B:D.167 GOL.7: 6 residues within 4Å: Chain A: G.166, V.167, H.168 Chain B: D.167, S.168, K.169 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.166, A:V.167, B:D.167 Water bridges: A:H.168 GOL.8: 5 residues within 4Å: Chain B: G.9, V.86, Y.88, G.100, G.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.88, B:Y.88 GOL.9: 6 residues within 4Å: Chain A: Q.39, Y.94 Chain B: Q.39, H.41, G.42, Q.43 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.39, A:Y.94, A:Y.94, B:G.42, B:Q.43 GOL.10: 5 residues within 4Å: Chain C: R.131, S.133, N.134, K.136, E.139 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.131, C:R.131, C:S.133, C:S.133 GOL.11: 6 residues within 4Å: Chain C: F.16, N.17, F.45, P.47, W.110 Ligands: NAG-FUC.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.17, C:P.47 GOL.12: 4 residues within 4Å: Chain A: Y.102 Chain B: Y.50, T.57 Chain C: Y.163 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.163, C:Y.163, B:T.57, B:T.57 GOL.13: 4 residues within 4Å: Chain C: F.21, A.22, S.23, N.124 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.21, C:S.23 GOL.14: 7 residues within 4Å: Chain C: V.177, Y.182 Chain D: R.45, E.46, T.106, W.107, P.108 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.46, D:T.106

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 3 residues within 4Å: Chain A: E.1, V.2, G.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.1, A:E.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huo, J. et al., Humoral responses against SARS-CoV-2 Omicron BA.2.11, BA.2.12.1 and BA.2.13 from vaccine and BA.1 serum. Cell Discov (2022)

Release Date

2022-11-23

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

D
C

Beta-27 heavy chain

Beta-27 light chain

Spike protein S1

Nanobody C1

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