SMTL ID : 6pxh.1 (1 other biounit)

Crystal Structure of MERS-CoV S1-NTD bound with G2 Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 1 residues within 4Å: Chain A: N.49 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: Q.20, D.24, N.87, M.144 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 7 residues within 4Å: Chain A: G.104, A.105, A.107, N.108, E.232, I.233, Y.257 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.257, A:Y.257

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 3 residues within 4Å: Chain A: F.148, N.149 Ligands: SO4.10 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: Y.1, I.169, N.219 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.5: 8 residues within 4Å: Chain A: Y.1, D.3, G.5, P.6, R.164, N.205, L.208, M.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.3, A:D.3, A:D.3 Hydrophobic interactions: A:M.223

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

NAG.7: 3 residues within 4Å: Chain A: N.138, G.142, M.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.138 NAG.8: 2 residues within 4Å: Chain A: R.204, N.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.204, A:R.204, A:N.227

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

SO4.9: 2 residues within 4Å: Chain A: R.45, T.46 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.46, A:T.46 Water bridges: A:T.46, A:T.46 SO4.10: 3 residues within 4Å: Chain A: R.146 Ligands: NAG-NAG.4, NAG-NAG.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.146 Salt bridges: A:R.146 SO4.11: 3 residues within 4Å: Chain A: H.74, A.75, R.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.75 Salt bridges: A:H.74, A:R.290 SO4.12: 3 residues within 4Å: Chain A: K.93, Q.94, K.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.94 Salt bridges: A:K.93, A:K.300 SO4.14: 5 residues within 4Å: Chain B: F.27, T.28, F.29, S.30, S.77 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.29, B:S.30 Water bridges: B:S.30, B:S.77, B:S.77 SO4.15: 2 residues within 4Å: Chain B: Q.1, G.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.1 Water bridges: B:Q.1, B:Q.1

1 x DHF: DIHYDROFOLIC ACID(Non-covalent)

DHF.13: 11 residues within 4Å: Chain A: W.27, P.28, R.29, A.106, G.111, T.112, I.123, A.292, W.293, A.294, A.295 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.27 Hydrogen bonds: A:R.29, A:T.112, A:T.112, A:W.293, A:W.293, A:A.295 Water bridges: A:R.29 pi-Stacking: A:W.27, A:W.27, A:W.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, N. et al., Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD. Cell Rep (2019)

Release Date

2019-09-25

Peptides

MERS-CoV S1-NTD: A
G2 heavy chain: B
G2 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

MERS-CoV S1-NTD

G2 heavy chain

G2 light chain

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