SMTL ID : 6hgb.1

Influenza A virus N6 neuraminidase native structure (Duck/England/56).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: N.5, T.7, K.154 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.65, L.358 Chain C: Y.387 Ligands: PO4.18 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: Y.387 Chain B: N.65, L.358 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: T.2, F.3, N.5, K.154 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.65, L.358 Chain D: Y.387 Ligands: PEG.48 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: Y.387 Chain D: N.65, L.358 Ligands: PEG.32 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.3: 19 residues within 4Å: Chain A: N.119, N.120 Chain C: N.14, S.15, D.250, R.284, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, V.315, L.374, G.375, S.376 Ligands: GOL.43, GOL.44 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.313, C:N.313, C:N.313, C:N.313, C:N.313, C:N.313, C:R.284 Water bridges: C:K.288, C:K.288

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.5: 17 residues within 4Å: Chain A: N.14, S.15, D.250, R.284, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, V.315, R.373, L.374, G.375 Chain B: N.119, N.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.313, A:N.313, A:N.313, A:R.373, A:R.373, A:N.313

2 x NAG- NAG- BMA- MAN- MAN- MAN: 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.8: 15 residues within 4Å: Chain C: N.120 Chain D: N.14, D.250, R.284, E.295, L.297, P.310, I.311, S.312, N.313, V.315, R.373, L.374, G.375, S.376 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.313, D:N.313, D:N.313, D:N.313, D:R.373, D:R.373, D:N.313, D:R.284 Water bridges: D:D.250, D:R.284, D:K.288, D:K.288 NAG-NAG-BMA-MAN-MAN-MAN.9: 16 residues within 4Å: Chain B: N.14, D.250, R.284, E.295, L.297, P.310, I.311, S.312, N.313, Q.314, V.315, L.374, G.375, S.376 Chain D: N.120 Ligands: PEG.34 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.313, B:N.313, B:N.313, B:D.250, B:R.284 Water bridges: B:R.373, B:D.250, B:D.250, B:K.288, B:K.288, B:K.288

25 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: R.26 Chain B: Q.55, H.63, N.65, G.66, T.67, S.72 Ligands: PEG.33 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: E.29, D.30, A.31, H.32, R.60 Chain C: D.30 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: R.144, A.166, E.196, E.197, R.212, N.214 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: R.169, L.188, A.189, G.190, A.192, Q.193 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain A: H.380 Chain B: F.74 Ligands: PEG.33 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain A: G.204, G.205, V.206, D.226 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: R.26 Chain D: H.63, N.65, G.66, T.67, S.72 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain B: D.70, R.71, W.98, S.99, I.142, R.144, E.147 Ligands: GOL.24 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain B: R.144, A.166, E.196, E.197, R.212, N.214, Y.325 Ligands: GOL.23 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain B: R.169, L.188, A.189, G.190, A.192, Q.193 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain B: N.318, N.321, H.380 Ligands: PEG.30 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain B: D.44, Q.46, G.47, R.49 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain A: H.63, N.65, G.66 Chain C: R.26 Ligands: PO4.18 Ligand excluded by PLIP GOL.39: 3 residues within 4Å: Chain C: N.167, N.168, W.215 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain C: R.169, A.170, L.188, A.189, G.190, A.192, Q.193 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain C: D.70, R.71, R.75, W.98, S.99, R.144, E.147 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain C: E.29, D.30, A.31, H.32, R.60 Chain D: D.30 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain C: R.284, I.286, E.295 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3, GOL.44 Ligand excluded by PLIP GOL.44: 7 residues within 4Å: Chain C: R.247, R.284, I.286, K.288, E.295 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3, GOL.43 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain C: D.44, G.47, C.48, R.49, E.81 Ligand excluded by PLIP GOL.52: 6 residues within 4Å: Chain C: H.63, N.65, G.66, T.67, S.72 Chain D: R.26 Ligand excluded by PLIP GOL.53: 7 residues within 4Å: Chain D: R.144, A.166, E.196, E.197, R.212, N.214 Ligands: GOL.54 Ligand excluded by PLIP GOL.54: 8 residues within 4Å: Chain D: D.70, R.71, W.98, S.99, R.144, E.147, E.197 Ligands: GOL.53 Ligand excluded by PLIP GOL.55: 7 residues within 4Å: Chain D: R.169, A.170, L.188, A.189, G.190, A.192, Q.193 Ligand excluded by PLIP GOL.56: 5 residues within 4Å: Chain D: D.44, Q.46, G.47, C.48, R.49 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-covalent)

CA.17: 5 residues within 4Å: Chain A: D.213, G.217, D.244, P.267, G.268 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.244, A:P.267, H2O.3, H2O.8 CA.28: 4 residues within 4Å: Chain B: D.213, G.217, D.244, P.267 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.244, B:P.267, H2O.22, H2O.24 CA.46: 4 residues within 4Å: Chain C: D.213, G.217, D.244, P.267 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.244, C:P.267, H2O.37, H2O.38 CA.57: 5 residues within 4Å: Chain D: D.213, G.217, D.244, P.267, G.268 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.244, H2O.50, H2O.54

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.18: 4 residues within 4Å: Chain A: N.65, G.66 Ligands: NAG-NAG.2, GOL.38 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Water bridges: C:Y.387, C:Y.387, C:Y.387, C:Y.387, A:N.65, A:N.65, A:N.65 Hydrogen bonds: A:N.65 PO4.19: 4 residues within 4Å: Chain A: E.186, A.189, T.231, H.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.232 Salt bridges: A:H.232 PO4.29: 3 residues within 4Å: Chain B: W.138, K.173, I.185 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.173

19 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.20: 8 residues within 4Å: Chain A: E.81, Q.84, Y.89, N.90 Chain B: Y.89, N.90, T.91, R.92 Ligand excluded by PLIP PEG.30: 6 residues within 4Å: Chain B: N.321, H.380, G.382, A.383 Chain D: F.74 Ligands: GOL.26 Ligand excluded by PLIP PEG.31: 9 residues within 4Å: Chain B: H.17, D.331, K.336, N.340, C.342, C.368, G.369 Chain D: P.131, E.134 Ligand excluded by PLIP PEG.32: 5 residues within 4Å: Chain B: E.384, I.386, Y.387 Ligands: NAG-NAG.10, NAG-NAG.10 Ligand excluded by PLIP PEG.33: 6 residues within 4Å: Chain A: W.377 Chain B: R.71, S.72, P.73 Ligands: GOL.11, GOL.15 Ligand excluded by PLIP PEG.34: 4 residues within 4Å: Chain B: K.240, G.309, P.310 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.9 Ligand excluded by PLIP PEG.35: 5 residues within 4Å: Chain B: G.263, S.264, P.265, D.266, P.267 Ligand excluded by PLIP PEG.36: 3 residues within 4Å: Chain B: K.181, I.182, Q.183 Ligand excluded by PLIP PEG.37: 6 residues within 4Å: Chain B: A.139, N.141, G.164, P.165, R.169, A.170 Ligand excluded by PLIP PEG.47: 10 residues within 4Å: Chain A: P.131, I.132, E.134 Chain C: H.17, D.331, K.336, N.340, C.342, C.368, G.369 Ligand excluded by PLIP PEG.48: 5 residues within 4Å: Chain D: E.384, I.386, Y.387 Ligands: NAG-NAG.7, NAG-NAG.7 Ligand excluded by PLIP PEG.49: 2 residues within 4Å: Chain C: P.9, E.337 Ligand excluded by PLIP PEG.50: 7 residues within 4Å: Chain C: S.246, G.262, G.263, S.264, P.265, D.266, P.267 Ligand excluded by PLIP PEG.58: 6 residues within 4Å: Chain D: I.135, P.136, S.137, W.138, K.173, I.185 Ligand excluded by PLIP PEG.59: 11 residues within 4Å: Chain C: P.131 Chain D: H.17, L.19, C.48, F.329, D.331, K.336, N.340, C.342, C.368, G.369 Ligand excluded by PLIP PEG.60: 5 residues within 4Å: Chain D: R.1, Q.46, H.104, G.106, M.107 Ligand excluded by PLIP PEG.61: 5 residues within 4Å: Chain D: Q.307, S.308, G.309, P.310, I.311 Ligand excluded by PLIP PEG.62: 6 residues within 4Å: Chain D: A.139, N.141, G.164, P.165, R.169, A.170 Ligand excluded by PLIP PEG.63: 8 residues within 4Å: Chain C: R.49, S.79, W.80, N.90, T.91, R.92 Chain D: E.81, Q.84 Ligand excluded by PLIP

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

NAG.21: 3 residues within 4Å: Chain B: T.2, N.5, K.154 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.2 Hydrogen bonds: B:N.5 NAG.51: 4 residues within 4Å: Chain D: T.2, F.3, N.5, K.154 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.2, D:F.3, D:N.5 Water bridges: D:F.3, D:N.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salinger, M.T. et al., High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site. (In preparation). To Be Published

Release Date

2018-09-05

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Neuraminidase

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