SMTL ID : 7l0n.2 (1 other biounit)

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

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

NAG-NAG-BMA-MAN-FUC.1: 14 residues within 4Å: Chain A: Y.50, T.57 Chain B: Y.32, R.98, Y.100, I.111, G.112, D.115 Chain F: F.11, G.12, F.15, N.16, V.40 Ligands: CL.31 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.50, B:Y.100 Hydrogen bonds: B:Y.32, B:Y.32, B:D.115, B:D.115

19 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: L.13, R.18, T.20 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: T.97, F.98 Chain B: W.47 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain B: Q.65 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain C: S.7, R.24 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain C: R.18, T.74 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain D: F.27, T.28, Y.32 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: V.170, H.171, T.172 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain D: S.84, R.86 Ligands: NAG.17 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain D: T.57, Y.58 Chain F: N.43, F.50 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain D: S.100, Y.103 Chain F: K.59 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain E: N.176, Y.178, R.201 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain E: R.151, W.459 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain E: K.291, W.310 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain E: H.16, D.20 Chain F: S.167 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain E: N.31, N.43 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain E: E.5, T.9 Chain F: Y.146, A.148 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain F: P.3, N.4 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain F: F.50 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain F: S.44, F.47 Ligands: NAG-NAG-BMA-MAN-FUC.1 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain C: K.39, K.42, K.45 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:K.39, C:K.42, C:K.45

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

PG4.8: 5 residues within 4Å: Chain C: P.59, S.60, R.61, S.77, Q.79 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.60, C:R.61, C:R.61, C:Q.79

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 4 residues within 4Å: Chain E: H.356, E.357, H.360, E.384 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.356, E:H.360, E:E.384, E:E.384

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

NAG.15: 3 residues within 4Å: Chain E: S.402, D.525, N.528 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.402, E:S.402, E:S.402, E:N.528 NAG.16: 3 residues within 4Å: Chain E: K.8, N.72, T.74 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.74 NAG.17: 5 residues within 4Å: Chain D: R.86 Chain E: K.291, E.294, N.304 Ligands: CL.11 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.86, D:R.86, E:K.291 NAG.18: 5 residues within 4Å: Chain E: N.35, T.37, E.39, N.40, Q.322 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.35, E:E.39, E:N.40 NAG.19: 3 residues within 4Å: Chain E: E.412, D.413, N.414 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.413, E:N.414

2 x NA: SODIUM ION(Non-functional Binders)

NA.21: 2 residues within 4Å: Chain E: D.198, N.560 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.560 NA.24: 2 residues within 4Å: Chain E: Q.513, A.514 No protein-ligand interaction detected (PLIP)

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.29: 5 residues within 4Å: Chain F: S.22, Y.24, N.123, L.125, I.141 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.22, F:Y.24, F:N.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomson, E.C. et al., Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell (2021)

Release Date

2021-02-17

Peptides

Monoclonal antibody S309 Fab light chain: A
Monoclonal antibody S309 Fab heavy chain: B
Monoclonal antibody S304 Fab light chain: C
Monoclonal antibody S304 Fab heavy chain: D
Angiotensin-converting enzyme 2: E
Spike protein S1: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
N

D
M

E
F

F
S

Monoclonal antibody S309 Fab light chain

Monoclonal antibody S309 Fab heavy chain

Monoclonal antibody S304 Fab light chain

Monoclonal antibody S304 Fab heavy chain

Angiotensin-converting enzyme 2

Spike protein S1

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