SMTL ID : 7m5e.1

MERS-CoV S bound to the broadly neutralizing B6 Fab fragment (C3 refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.50 Å

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

NAG-NAG-BMA-MAN.1: 8 residues within 4Å: Chain A: D.34, G.36, P.37, R.195, N.236, L.239, N.240, M.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.34, A:D.34, A:D.34 Hydrophobic interactions: A:M.254 NAG-NAG-BMA-MAN.5: 8 residues within 4Å: Chain A: S.790, P.1221, Q.1222, V.1223, Y.1225, Q.1226, N.1227 Chain C: E.1006 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.1006 Hydrophobic interactions: A:P.1221 NAG-NAG-BMA-MAN.11: 8 residues within 4Å: Chain B: D.34, G.36, P.37, R.195, N.236, L.239, N.240, M.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.34, B:D.34, B:D.34 Hydrophobic interactions: B:M.254 NAG-NAG-BMA-MAN.15: 8 residues within 4Å: Chain A: E.1006 Chain B: S.790, P.1221, Q.1222, V.1223, Y.1225, Q.1226, N.1227 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.1006 Hydrophobic interactions: B:P.1221 NAG-NAG-BMA-MAN.21: 8 residues within 4Å: Chain C: D.34, G.36, P.37, R.195, N.236, L.239, N.240, M.254 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.34, C:D.34, C:D.34 Hydrophobic interactions: C:M.254 NAG-NAG-BMA-MAN.25: 8 residues within 4Å: Chain B: E.1006 Chain C: S.790, P.1221, Q.1222, V.1223, Y.1225, Q.1226, N.1227 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.1006 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(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.12: 2 residues within 4Å: Chain B: I.200, N.250 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.80, V.343 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: Q.51, D.55, N.118, Q.121 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain B: R.235, N.258 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: I.200, N.250 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain C: N.80, V.343 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain C: Q.51, D.55, N.118, Q.121 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 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

NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 11 residues within 4Å: Chain A: N.424, T.426, K.427, K.601 Chain B: K.516, L.520, D.524, E.527, Y.554, R.556, W.567 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.556, B:K.516 NAG-NAG-BMA-MAN-MAN-MAN-MAN.13: 11 residues within 4Å: Chain B: N.424, T.426, K.427, K.601 Chain C: K.516, L.520, D.524, E.527, 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.23: 11 residues within 4Å: Chain A: K.516, L.520, D.524, E.527, Y.554, R.556, W.567 Chain C: N.424, T.426, K.427, K.601 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.556, A: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

NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: N.884, T.886, Q.1023 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain B: N.884, T.886, Q.1023 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 3 residues within 4Å: Chain C: N.884, T.886, Q.1023 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

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: 5 residues within 4Å: Chain A: F.179, N.180 Chain B: V.541, S.542, V.544 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.18: 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.19: 5 residues within 4Å: Chain B: F.179, N.180 Chain C: V.541, S.542, V.544 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.28: 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.29: 5 residues within 4Å: Chain A: V.541, S.542, V.544 Chain C: F.179, N.180 No protein-ligand interaction detected (PLIP)

3 x FOL: FOLIC ACID(Non-covalent)

FOL.31: 12 residues within 4Å: Chain A: W.58, P.59, R.60, P.61, A.137, G.142, T.143, I.154, A.323, W.324, A.325, A.326 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.58 Hydrogen bonds: A:P.59, A:R.60, A:T.143, A:T.143, A:T.143, A:W.324, A:A.326 Salt bridges: A:H.95 pi-Stacking: A:W.58, A:W.58, A:W.58 FOL.40: 12 residues within 4Å: Chain B: W.58, P.59, R.60, P.61, A.137, G.142, T.143, I.154, A.323, W.324, A.325, A.326 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.58 Hydrogen bonds: B:P.59, B:R.60, B:T.143, B:T.143, B:T.143, B:W.324, B:A.326 Salt bridges: B:H.95 pi-Stacking: B:W.58, B:W.58, B:W.58 FOL.49: 12 residues within 4Å: Chain C: W.58, P.59, R.60, P.61, A.137, G.142, T.143, I.154, A.323, W.324, A.325, A.326 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.58 Hydrogen bonds: C:P.59, C:R.60, C:T.143, C:T.143, C:T.143, C:W.324, C:A.326 Salt bridges: C:H.95 pi-Stacking: C:W.58, C:W.58, C:W.58

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

NAG.32: 1 residues within 4Å: Chain A: N.501 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.606 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: N.633, N.661, Y.663 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain A: L.721, Q.722, N.733, S.735, L.773 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.788 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: N.799, N.1159 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain A: N.169, F.170, S.171, F.179 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.501 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.606 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: N.633, N.661, Y.663 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain B: L.721, Q.722, N.733, S.735, L.773 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.788 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: N.799, N.1159 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain B: N.169, F.170, S.171, F.179 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: 5 residues within 4Å: Chain C: L.721, Q.722, N.733, S.735, 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: 4 residues within 4Å: Chain C: N.169, F.170, S.171, F.179 Ligand excluded by PLIP

3 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.39: 9 residues within 4Å: Chain A: Q.50, F.53, H.105, A.106, F.115, I.146, S.147, S.149, R.321 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.53, A:F.115, A:I.146 Hydrogen bonds: A:Q.50, A:H.105, A:A.106, A:A.106, A:I.146, A:R.321, A:R.321 SIA.48: 9 residues within 4Å: Chain B: Q.50, F.53, H.105, A.106, F.115, I.146, S.147, S.149, R.321 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.53, B:F.115, B:I.146 Hydrogen bonds: B:Q.50, B:H.105, B:A.106, B:A.106, B:I.146, B:R.321, B:R.321 SIA.57: 9 residues within 4Å: Chain C: Q.50, F.53, H.105, A.106, F.115, I.146, S.147, S.149, R.321 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.53, C:F.115, C:I.146 Hydrogen bonds: C:Q.50, C:H.105, C:A.106, C:A.106, C:I.146, C:R.321, C:R.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauer, M.M. et al., Structural basis for broad coronavirus neutralization. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-05-26

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

Spike glycoprotein

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