SMTL ID : 1v3d.2 (1 other biounit)

Structure of the hemagglutinin-neuraminidase from human parainfluenza virus type III: complex with NEU5AC2EN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-octamer

Ligands

8 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.210, T.212, W.310 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.210, T.212, W.310 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.210, T.212, W.310 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain D: N.210, T.212, W.310 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain E: N.210, T.212, W.310 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain F: N.210, T.212, W.310 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain G: N.210, T.212, W.310 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 3 residues within 4Å: Chain H: N.210, T.212, W.310 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.167 Ligand excluded by PLIP NAG.4: 5 residues within 4Å: Chain A: L.381, N.382, R.383, T.384 Chain B: S.413 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain B: N.166, N.167, I.250 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain B: N.382, R.383, T.384 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain C: N.167 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain C: L.381, N.382, R.383, T.384 Chain D: S.413 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: N.166, N.167, I.250 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain D: N.382, R.383, T.384 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain E: N.167 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain E: L.381, N.382, R.383, T.384 Chain F: S.413 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain F: N.166, N.167, I.250 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain F: N.382, R.383, T.384 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain G: N.167 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain G: L.381, N.382, R.383, T.384 Chain H: S.413 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain H: N.166, N.167, I.250 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain H: N.382, R.383, T.384 Ligand excluded by PLIP

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.138, S.141, P.142, G.143, A.175 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.138, A:S.141, A:S.141, A:G.143, A:A.175 CA.10: 4 residues within 4Å: Chain B: D.138, S.141, G.143, A.175 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.138, B:D.138, B:S.141, B:G.143, B:A.175 CA.17: 5 residues within 4Å: Chain C: D.138, S.141, P.142, G.143, A.175 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.138, C:S.141, C:S.141, C:G.143, C:A.175 CA.22: 4 residues within 4Å: Chain D: D.138, S.141, G.143, A.175 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.138, D:D.138, D:S.141, D:G.143, D:A.175 CA.29: 5 residues within 4Å: Chain E: D.138, S.141, P.142, G.143, A.175 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.138, E:S.141, E:S.141, E:G.143, E:A.175 CA.34: 4 residues within 4Å: Chain F: D.138, S.141, G.143, A.175 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.138, F:D.138, F:S.141, F:G.143, F:A.175 CA.41: 5 residues within 4Å: Chain G: D.138, S.141, P.142, G.143, A.175 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.138, G:S.141, G:S.141, G:G.143, G:A.175 CA.46: 4 residues within 4Å: Chain H: D.138, S.141, G.143, A.175 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.138, H:D.138, H:S.141, H:G.143, H:A.175

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

SO4.6: 4 residues within 4Å: Chain A: D.134, E.135, R.136, W.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.135, A:R.136 SO4.11: 5 residues within 4Å: Chain A: N.91, S.92 Chain B: H.104, T.105 Chain H: N.248 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 interactions with chain H Hydrogen bonds: B:T.105, A:S.92, A:S.92, H:N.248 Salt bridges: B:H.104 SO4.18: 4 residues within 4Å: Chain C: D.134, E.135, R.136, W.230 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.135, C:R.136 SO4.23: 5 residues within 4Å: Chain C: N.91, S.92 Chain D: H.104, T.105 Chain F: N.248 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F, 2 interactions with chain D Hydrogen bonds: C:S.92, C:S.92, F:N.248, D:T.105 Salt bridges: D:H.104 SO4.30: 4 residues within 4Å: Chain E: D.134, E.135, R.136, W.230 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.134, E:R.136 SO4.35: 5 residues within 4Å: Chain D: N.248 Chain E: N.91, S.92 Chain F: H.104, T.105 6 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: F:T.105, F:T.105, D:N.248, E:S.92, E:S.92 Salt bridges: F:H.104 SO4.42: 4 residues within 4Å: Chain G: D.134, E.135, R.136, W.230 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.134, G:R.136 SO4.47: 5 residues within 4Å: Chain B: N.248 Chain G: N.91, S.92 Chain H: H.104, T.105 6 PLIP interactions: 2 interactions with chain G, 3 interactions with chain H, 1 interactions with chain B Hydrogen bonds: G:S.92, G:S.92, H:T.105, H:T.105, B:N.248 Salt bridges: H:H.104

8 x DAN: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID(Non-covalent)

DAN.7: 8 residues within 4Å: Chain A: R.51, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.178 Hydrogen bonds: A:E.135, A:Y.196, A:Y.196, A:E.268, A:R.283, A:Y.389 Water bridges: A:E.135, A:E.268, A:R.283, A:R.283, A:R.283 Salt bridges: A:R.51, A:R.283, A:R.361 DAN.12: 8 residues within 4Å: Chain B: R.51, 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:Y.178 Hydrogen bonds: B:E.135, B:Y.196, B:Y.196, B:E.268, B:R.283, B:Y.389 Water bridges: B:R.51, B:R.51, B:E.135, B:E.135, B:E.268, B:R.283, B:R.283 Salt bridges: B:R.51, B:R.283, B:R.361 DAN.19: 8 residues within 4Å: Chain C: R.51, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Y.178 Hydrogen bonds: C:E.135, C:Y.196, C:Y.196, C:E.268, C:R.283, C:Y.389 Water bridges: C:E.135, C:E.268, C:R.283, C:R.283, C:R.283 Salt bridges: C:R.51, C:R.283, C:R.361 DAN.24: 8 residues within 4Å: Chain D: R.51, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:Y.178 Hydrogen bonds: D:E.135, D:Y.196, D:Y.196, D:E.268, D:R.283, D:Y.389 Water bridges: D:R.51, D:R.51, D:E.135, D:E.135, D:E.268, D:R.283, D:R.283 Salt bridges: D:R.51, D:R.283, D:R.361 DAN.31: 8 residues within 4Å: Chain E: R.51, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:Y.178 Hydrogen bonds: E:E.135, E:Y.196, E:Y.196, E:E.268, E:R.283 Water bridges: E:E.135, E:Y.139, E:R.283, E:R.283, E:R.283, E:T.285, E:T.285 Salt bridges: E:R.51, E:R.283, E:R.361 DAN.36: 8 residues within 4Å: Chain F: R.51, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:Y.178 Hydrogen bonds: F:E.135, F:Y.196, F:Y.196, F:E.268, F:R.283 Water bridges: F:R.51, F:R.51, F:E.135, F:E.268, F:R.283, F:R.283, F:T.285 Salt bridges: F:R.51, F:R.283, F:R.361 DAN.43: 8 residues within 4Å: Chain G: R.51, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:Y.178 Hydrogen bonds: G:E.135, G:Y.196, G:Y.196, G:E.268, G:R.283 Water bridges: G:E.135, G:Y.139, G:R.283, G:R.283, G:R.283, G:T.285, G:T.285 Salt bridges: G:R.51, G:R.283, G:R.361 DAN.48: 8 residues within 4Å: Chain H: R.51, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 16 PLIP interactions: 16 interactions with chain H Hydrophobic interactions: H:Y.178 Hydrogen bonds: H:E.135, H:Y.196, H:Y.196, H:E.268, H:R.283 Water bridges: H:R.51, H:R.51, H:E.135, H:E.268, H:R.283, H:R.283, H:T.285 Salt bridges: H:R.51, H:R.283, H:R.361

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lawrence, M.C. et al., Structure of the Haemagglutinin-neuraminidase from Human Parainfluenza Virus Type III. J.Mol.Biol. (2004)

Release Date

2004-02-03

Peptides

hemagglutinin-neuraminidase glycoprotein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

hemagglutinin-neuraminidase glycoprotein

Related Entries With Identical Sequence