SMTL ID : 6cf5.1

Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in complex with small molecule N-Cyclohexyltaurine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-3-3-mer

Ligands

3 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: 5 residues within 4Å: Chain A: N.169, N.240, D.241, A.242 Chain E: S.221 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: S.221 Chain C: N.169, N.240, D.241, A.242 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.240 NAG-NAG.3: 4 residues within 4Å: Chain C: S.221 Chain E: N.169, N.240, A.242 No protein-ligand interaction detected (PLIP)

3 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.4: 8 residues within 4Å: Chain A: L.133, V.135, S.136, S.137, W.153, I.155, L.194, Q.226 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.153, A:W.153, A:I.155, A:L.194 Hydrogen bonds: A:V.135, A:S.137, A:Q.226 Water bridges: A:S.145 NHE.12: 9 residues within 4Å: Chain C: L.133, V.135, S.136, S.137, S.145, W.153, I.155, L.194, Q.226 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.153, C:I.155 Hydrogen bonds: C:V.135, C:S.137, C:S.145, C:Q.226, C:Q.226 NHE.19: 8 residues within 4Å: Chain E: L.133, V.135, S.136, S.137, W.153, I.155, L.194, Q.226 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:W.153, E:I.155 Hydrogen bonds: E:V.135, E:S.137, E:Q.226, E:Q.226 Water bridges: E:S.145

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

NAG.5: 3 residues within 4Å: Chain A: Q.19, K.26, N.27 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.26 Hydrogen bonds: A:N.27 Water bridges: A:N.27 NAG.13: 1 residues within 4Å: Chain C: N.290 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain C: K.26, N.27, R.314 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.26 Hydrogen bonds: C:N.27, C:R.314

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

PEG.6: 5 residues within 4Å: Chain A: Q.34 Chain B: V.52, N.53, I.56 Ligands: PEG.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.34 Water bridges: A:S.292 PEG.7: 3 residues within 4Å: Chain A: D.72, I.75, R.149 No protein-ligand interaction detected (PLIP) PEG.8: 4 residues within 4Å: Chain A: I.75, N.76, K.117, Y.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.76 PEG.10: 6 residues within 4Å: Chain A: C.8 Chain B: W.14, H.25, Y.34, N.135, C.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.34, B:Y.34, B:N.135 PEG.11: 5 residues within 4Å: Chain A: H.32, T.319 Chain B: W.21, T.49 Ligands: PEG.6 No protein-ligand interaction detected (PLIP) PEG.15: 4 residues within 4Å: Chain C: K.123, R.149, E.255, Y.256 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.119, C:E.255 PEG.17: 6 residues within 4Å: Chain C: C.8 Chain D: W.14, H.25, Y.34, N.135, C.137 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.34, D:N.135 Water bridges: D:E.11 PEG.18: 9 residues within 4Å: Chain B: L.2, R.106 Chain D: L.2, R.106, D.109, F.110 Chain F: L.2, R.106, D.109 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:R.106, D:R.106, F:R.106, F:R.106, F:D.109 PEG.20: 2 residues within 4Å: Chain E: Y.141, R.149 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.141

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: V.20, D.21, R.314, L.315, V.316 Chain B: N.104 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.21, A:D.21, A:R.314, A:V.316, B:N.104 Water bridges: A:R.314, A:R.314 GOL.16: 7 residues within 4Å: Chain C: V.20, D.21, R.314, L.315, V.316 Chain D: V.100, N.104 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:N.104, C:D.21, C:D.21, C:D.21, C:D.21, C:V.316 GOL.21: 6 residues within 4Å: Chain E: V.20, D.21, R.314, L.315, V.316 Chain F: N.104 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:N.104, E:D.21, E:V.316, E:V.316 GOL.22: 5 residues within 4Å: Chain E: A.62, D.92, L.93, F.99, Y.102 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:F.99, E:Y.102 Water bridges: E:F.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadam, R.U. et al., A small-molecule fragment that emulates binding of receptor and broadly neutralizing antibodies to influenza A hemagglutinin. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-04-04

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin

Hemagglutinin

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