SMTL ID : 6q06.1

MERS-CoV S structure in complex with 2,3-sialyl-N-acetyl-lactosamine

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG-NAG-BMA-MAN.1: 7 residues within 4Å: Chain A: D.34, G.36, P.37, R.195, N.236, L.239, M.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.34, A:D.34, A:D.34, A:D.34 Hydrophobic interactions: A:M.254 NAG-NAG-BMA-MAN.5: 7 residues within 4Å: Chain A: S.790, P.1221, Q.1222, V.1223, Y.1225, Q.1226, N.1227 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.1221 NAG-NAG-BMA-MAN.12: 7 residues within 4Å: Chain B: D.34, G.36, P.37, R.195, N.236, L.239, M.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.34, B:D.34, B:D.34, B:D.34 Hydrophobic interactions: B:M.254 NAG-NAG-BMA-MAN.16: 7 residues within 4Å: Chain B: S.790, P.1221, Q.1222, V.1223, Y.1225, Q.1226, N.1227 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.1221 NAG-NAG-BMA-MAN.23: 7 residues within 4Å: Chain C: D.34, G.36, P.37, R.195, N.236, L.239, M.254 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.34, C:D.34, C:D.34, C:D.34 Hydrophobic interactions: C:M.254 NAG-NAG-BMA-MAN.27: 7 residues within 4Å: Chain C: S.790, P.1221, Q.1222, V.1223, Y.1225, Q.1226, N.1227 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.1221

12 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: I.200, N.250 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.80, V.343 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: Q.51, D.55, N.118, Q.121 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain A: R.235, N.258 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: I.200, N.250 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.80, V.343 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain B: Q.51, D.55, N.118, Q.121 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain B: R.235, N.258 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: I.200, N.250 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain C: N.80, V.343 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain C: Q.51, D.55, N.118, Q.121 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain C: R.235, N.258 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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(Non-functional Binders)(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 10 residues within 4Å: Chain A: N.424, T.426, K.427, K.601 Chain C: K.516, L.520, D.524, Y.554, R.556, W.567 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.556, C:K.516 NAG-NAG-BMA-MAN-MAN-MAN-MAN.14: 10 residues within 4Å: Chain A: K.516, L.520, D.524, Y.554, R.556, W.567 Chain B: N.424, T.426, K.427, K.601 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.556, A:K.516 NAG-NAG-BMA-MAN-MAN-MAN-MAN.25: 10 residues within 4Å: Chain B: K.516, L.520, D.524, Y.554, R.556, W.567 Chain C: N.424, T.426, K.427, K.601 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.556, B:K.516

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(Non-functional Binders)(Post Translational Modification)

NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: N.884, T.886 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 2 residues within 4Å: Chain B: N.884, T.886 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 2 residues within 4Å: Chain C: N.884, T.886 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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(Non-covalent)(Post Translational Modification)(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN.8: 7 residues within 4Å: Chain A: G.135, A.136, A.138, N.139, E.263, I.264, Y.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 4 residues within 4Å: Chain A: F.179, N.180 Chain C: V.541, S.542 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 7 residues within 4Å: Chain B: G.135, A.136, A.138, N.139, E.263, I.264, Y.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.20: 4 residues within 4Å: Chain A: V.541, S.542 Chain B: F.179, N.180 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.30: 7 residues within 4Å: Chain C: G.135, A.136, A.138, N.139, E.263, I.264, Y.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.31: 4 residues within 4Å: Chain B: V.541, S.542 Chain C: F.179, N.180 No protein-ligand interaction detected (PLIP)

3 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)(Non-functional Binders)

GAL-SIA.11: 9 residues within 4Å: Chain A: Q.50, F.53, H.105, A.106, F.115, I.146, S.147, Q.318, R.321 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.53, A:F.115 Hydrogen bonds: A:Q.50, A:A.106, A:A.106, A:I.146, A:R.321, A:R.321 GAL-SIA.22: 9 residues within 4Å: Chain B: Q.50, F.53, H.105, A.106, F.115, I.146, S.147, Q.318, R.321 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.53, B:F.115 Hydrogen bonds: B:Q.50, B:A.106, B:A.106, B:I.146, B:R.321, B:R.321 GAL-SIA.33: 9 residues within 4Å: Chain C: Q.50, F.53, H.105, A.106, F.115, I.146, S.147, Q.318, R.321 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.53, C:F.115 Hydrogen bonds: C:Q.50, C:A.106, C:A.106, C:I.146, C:R.321, C:R.321

21 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)(Post Translational Modification)(Non-covalent)

NAG.34: 1 residues within 4Å: Chain A: N.501 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.606 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: N.633, N.661, Y.663 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: L.721, Q.722, N.733, L.773 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.788 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.799, N.1159 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain A: N.169, F.170, S.171, G.173, R.177 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.501 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.606 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: N.633, N.661, Y.663 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: L.721, Q.722, N.733, L.773 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.788 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: N.799, N.1159 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain B: N.169, F.170, S.171, G.173, R.177 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.501 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.606 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: N.633, N.661, Y.663 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: L.721, Q.722, N.733, L.773 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.788 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: N.799, N.1159 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain C: N.169, F.170, S.171, G.173, R.177 Ligand excluded by PLIP

3 x FOL: FOLIC ACID(Non-functional Binders)(Non-covalent)

FOL.41: 13 residues within 4Å: Chain A: W.58, P.59, R.60, P.61, H.95, A.137, G.142, T.143, I.154, A.323, W.324, A.325, A.326 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.58, A:P.59 Hydrogen bonds: A:P.59, A:R.60, A:T.143, A:T.143, A:W.324, A:W.324, A:A.326 Water bridges: A:I.145 Salt bridges: A:H.95 pi-Stacking: A:W.58, A:W.58, A:W.58 FOL.49: 13 residues within 4Å: Chain B: W.58, P.59, R.60, P.61, H.95, A.137, G.142, T.143, I.154, A.323, W.324, A.325, A.326 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.58, B:P.59 Hydrogen bonds: B:P.59, B:R.60, B:T.143, B:T.143, B:W.324, B:W.324, B:A.326 Water bridges: B:I.145 Salt bridges: B:H.95 pi-Stacking: B:W.58, B:W.58, B:W.58 FOL.57: 13 residues within 4Å: Chain C: W.58, P.59, R.60, P.61, H.95, A.137, G.142, T.143, I.154, A.323, W.324, A.325, A.326 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.58, C:P.59 Hydrogen bonds: C:P.59, C:R.60, C:T.143, C:T.143, C:W.324, C:W.324, C:A.326 Water bridges: C:I.145 Salt bridges: C:H.95 pi-Stacking: C:W.58, C:W.58, C:W.58

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Park, Y.J. et al., Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-12-11

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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