SMTL ID : 5kv8.1

Crystal structure of a hPIV haemagglutinin-neuraminidase-inhibitor complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

8 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.1: 4 residues within 4Å: Chain A: N.210, T.212, W.310 Ligands: NDG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.210 NDG.2: 3 residues within 4Å: Chain A: W.310 Ligands: NDG.1, BMA.4 No protein-ligand interaction detected (PLIP) NDG.3: 3 residues within 4Å: Chain A: R.381, N.382, T.384 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.381, A:N.382 NDG.10: 3 residues within 4Å: Chain A: T.161, R.162, N.167 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.161 Hydrogen bonds: A:N.167 Water bridges: A:R.162, A:N.167 NDG.12: 4 residues within 4Å: Chain B: N.210, T.212, W.310 Ligands: NDG.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.210 NDG.13: 3 residues within 4Å: Chain B: W.310 Ligands: NDG.12, BMA.15 No protein-ligand interaction detected (PLIP) NDG.14: 3 residues within 4Å: Chain B: R.381, N.382, T.384 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.382, B:T.384 NDG.22: 3 residues within 4Å: Chain B: T.161, R.162, N.167 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.161 Hydrogen bonds: B:N.167

2 x BMA: beta-D-mannopyranose(Non-functional Binders)(Non-covalent)

BMA.4: 1 residues within 4Å: Ligands: NDG.2 No protein-ligand interaction detected (PLIP) BMA.15: 4 residues within 4Å: Chain B: W.310, T.372 Ligands: NDG.13, MAN.23 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.138, S.141, G.143, A.175 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.138, A:D.138, A:S.141, A:S.141, A:G.143 CA.16: 4 residues within 4Å: Chain B: D.138, S.141, G.143, A.175 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.138, B:D.138, B:S.141, B:G.143, H2O.16

2 x 6Y6: 2,6-anhydro-3,4,5-trideoxy-4-[4-(methoxymethyl)-1H-1,2,3-triazol-1-yl]-5-[(2-methylpropanoyl)amino]-D-glycero-D-galacto -non-2-enonic acid(Non-covalent)

6Y6.6: 12 residues within 4Å: Chain A: R.51, T.52, N.67, I.69, K.113, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:E.135, A:Y.178, A:Y.178 Hydrogen bonds: A:Y.196, A:Y.196, A:E.268, A:R.283 Water bridges: A:R.51, A:S.114, A:E.135, A:E.135, A:E.268, A:R.283, A:R.283, A:R.283, A:T.285, A:T.285, A:R.361 Salt bridges: A:R.51, A:R.283, A:R.361 6Y6.17: 14 residues within 4Å: Chain B: R.51, T.52, N.67, I.69, C.73, D.75, K.113, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:E.135, B:Y.178 Hydrogen bonds: B:Y.196, B:Y.196, B:E.268, B:R.283, B:Y.389 Water bridges: B:S.114, B:S.114, B:E.135, B:Y.139, B:E.268, B:E.268, B:R.283 Salt bridges: B:R.51, B:R.283, B:R.361

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 7 residues within 4Å: Chain A: L.120, Y.125, G.189, K.190, I.191, V.243, K.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.191, A:V.243 EDO.8: 5 residues within 4Å: Chain A: W.324, D.356, S.357, Q.358, R.374 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.358, A:R.374 Water bridges: A:W.324, A:R.374, A:R.374 EDO.9: 4 residues within 4Å: Chain A: F.106, N.107, D.110 Chain B: S.92 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.92, A:N.107, A:D.110, A:D.110 EDO.18: 5 residues within 4Å: Chain B: W.324, D.356, S.357, Q.358, R.374 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.356, B:Q.358, B:R.374 Water bridges: B:W.324 EDO.19: 6 residues within 4Å: Chain B: L.120, Y.125, G.189, K.190, I.191, V.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.191, B:V.243 Water bridges: B:G.189 EDO.20: 2 residues within 4Å: Chain B: G.213, P.215 No protein-ligand interaction detected (PLIP)

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.11: 9 residues within 4Å: Chain A: S.103, H.104, T.105, I.158 Chain B: T.89, V.90, N.91, D.97, N.99 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.89, B:T.89, B:N.99, A:T.105, A:T.105 Salt bridges: A:H.104, A:H.104

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

SO4.21: 8 residues within 4Å: Chain A: N.410, H.411, K.412, S.413 Chain B: H.411, K.412, S.413, L.414 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.412, A:S.413, A:S.413, B:K.412, B:S.413, B:S.413, B:L.414 Water bridges: B:S.413, B:S.413

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.23: 4 residues within 4Å: Chain B: W.310, A.371, T.372 Ligands: BMA.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.370, B:T.370, B:T.372 Water bridges: B:A.371, B:T.372, B:T.372

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 9 residues within 4Å: Chain A: P.37, T.89, V.90, N.91, D.97, N.99 Chain B: S.103, H.104, T.105 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.89, A:V.90, A:D.97, A:N.99, B:S.103, B:T.105, B:T.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dirr, L. et al., The impact of the butterfly effect on human parainfluenza virus haemagglutinin-neuraminidase inhibitor design. Sci Rep (2017)

Release Date

2017-07-12

Peptides

Hemagglutinin-neuraminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hemagglutinin-neuraminidase