SMTL ID : 7ly3.1 (1 other biounit)

Crystal structure of SARS-CoV-2 S NTD bound to S2M28 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x NAG- NAG- BMA- FUC: 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-FUC.1: 4 residues within 4Å: Chain A: N.36 Chain B: S.56, N.57, R.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.3: 7 residues within 4Å: Chain A: N.141, T.143, N.144, V.146, E.173, F.176, Y.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.144

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

NAG-FUC.2: 4 residues within 4Å: Chain A: Y.47, N.80, T.82, Y.288 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.288 Hydrogen bonds: A:Y.47, A:Y.47 NAG-FUC.4: 3 residues within 4Å: Chain A: E.151, N.183, N.184 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.183

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.5: 3 residues within 4Å: Chain A: N.299, E.300, N.301 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: G.251, N.253 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: H.165, N.168, M.172 No protein-ligand interaction detected (PLIP)

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.8: 2 residues within 4Å: Chain A: R.265, S.266 No protein-ligand interaction detected (PLIP)

1 x XYL: Xylitol(Non-covalent)

XYL.9: 6 residues within 4Å: Chain A: Y.57, D.59, K.60, E.243, P.244, G.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.59, A:E.243, A:G.302

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

SO4.10: 3 residues within 4Å: Chain B: G.26, F.27, N.77 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.26, B:F.27, B:F.27, B:N.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell (2021)

Release Date

2021-04-14

Peptides

Spike protein S1: A
S2M28 Fab Heavy Chain: B
S2M28 Fab Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
C

Spike protein S1

S2M28 Fab Heavy Chain

S2M28 Fab Light Chain

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