SMTL ID : 6pd3.1

Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 5.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: W.75, K.128, N.161, Y.269 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: S.147, S.148, Q.237 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: S.136, W.137, S.138, S.139, H.140, R.177 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: D.198, A.199 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: Q.130, P.133, K.134, S.135 Ligand excluded by PLIP SO4.6: 6 residues within 4Å: Chain A: G.315, C.317, K.319, T.406, Q.407 Chain C: D.435 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: L.144, G.145, V.146, W.164, L.205 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: H.23, N.25, T.42, H.43, G.331, W.366 Ligands: GOL.13 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: P.173, T.174 Ligand excluded by PLIP SO4.10: 8 residues within 4Å: Chain A: N.440, M.447 Chain B: N.440, M.447 Chain C: N.440, M.447 Ligands: SO4.29, SO4.48 Ligand excluded by PLIP SO4.11: 1 residues within 4Å: Ligands: NAG.18 Ligand excluded by PLIP SO4.12: 1 residues within 4Å: Ligands: NAG.17 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: W.75, K.128, N.161, Y.269 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: S.147, S.148, Q.237 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain B: S.136, W.137, S.138, S.139, H.140, R.177 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain B: D.198, A.199 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: Q.130, P.133, K.134, S.135 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain A: D.435 Chain B: G.315, C.317, K.319, T.406, Q.407 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain B: L.144, G.145, V.146, W.164, L.205 Ligand excluded by PLIP SO4.27: 7 residues within 4Å: Chain B: H.23, N.25, T.42, H.43, G.331, W.366 Ligands: GOL.32 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: P.173, T.174 Ligand excluded by PLIP SO4.29: 8 residues within 4Å: Chain A: N.440, M.447 Chain B: N.440, M.447 Chain C: N.440, M.447 Ligands: SO4.10, SO4.48 Ligand excluded by PLIP SO4.30: 1 residues within 4Å: Ligands: NAG.37 Ligand excluded by PLIP SO4.31: 1 residues within 4Å: Ligands: NAG.36 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain C: W.75, K.128, N.161, Y.269 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain C: S.147, S.148, Q.237 Ligand excluded by PLIP SO4.41: 6 residues within 4Å: Chain C: S.136, W.137, S.138, S.139, H.140, R.177 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain C: D.198, A.199 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain C: Q.130, P.133, K.134, S.135 Ligand excluded by PLIP SO4.44: 6 residues within 4Å: Chain B: D.435 Chain C: G.315, C.317, K.319, T.406, Q.407 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain C: L.144, G.145, V.146, W.164, L.205 Ligand excluded by PLIP SO4.46: 7 residues within 4Å: Chain C: H.23, N.25, T.42, H.43, G.331, W.366 Ligands: GOL.51 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain C: P.173, T.174 Ligand excluded by PLIP SO4.48: 8 residues within 4Å: Chain A: N.440, M.447 Chain B: N.440, M.447 Chain C: N.440, M.447 Ligands: SO4.10, SO4.29 Ligand excluded by PLIP SO4.49: 1 residues within 4Å: Ligands: NAG.56 Ligand excluded by PLIP SO4.50: 1 residues within 4Å: Ligands: NAG.55 Ligand excluded by PLIP

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain A: H.43, T.330, W.366, V.393, T.394 Ligands: SO4.8 No protein-ligand interaction detected (PLIP) GOL.14: 7 residues within 4Å: Chain A: A.381, D.382, K.383, E.384, E.495, R.498, N.499 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.382, A:D.382, A:K.383, A:E.384, A:E.495 GOL.15: 7 residues within 4Å: Chain A: S.71, A.73, D.103, L.104, D.109, F.110, Y.113 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.71, A:S.71, A:D.103, A:F.110, A:F.110 GOL.32: 6 residues within 4Å: Chain B: H.43, T.330, W.366, V.393, T.394 Ligands: SO4.27 No protein-ligand interaction detected (PLIP) GOL.33: 7 residues within 4Å: Chain B: A.381, D.382, K.383, E.384, E.495, R.498, N.499 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.382, B:D.382, B:K.383, B:E.384, B:E.495 GOL.34: 7 residues within 4Å: Chain B: S.71, A.73, D.103, L.104, D.109, F.110, Y.113 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.71, B:S.71, B:D.103, B:F.110, B:F.110 GOL.51: 6 residues within 4Å: Chain C: H.43, T.330, W.366, V.393, T.394 Ligands: SO4.46 No protein-ligand interaction detected (PLIP) GOL.52: 7 residues within 4Å: Chain C: A.381, D.382, K.383, E.384, E.495, R.498, N.499 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.382, C:D.382, C:K.383, C:E.384, C:E.495 GOL.53: 7 residues within 4Å: Chain C: S.71, A.73, D.103, L.104, D.109, F.110, Y.113 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.71, C:S.71, C:D.103, C:F.110, C:F.110

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

NAG.16: 2 residues within 4Å: Chain A: K.37, N.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.37 NAG.17: 4 residues within 4Å: Chain A: N.180, N.251 Chain C: S.232 Ligands: SO4.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.180, A:N.251 NAG.18: 6 residues within 4Å: Chain A: E.492, E.495, S.496, N.499, T.501 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.492, A:E.495, A:T.501 NAG.19: 1 residues within 4Å: Chain A: N.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.169 NAG.35: 2 residues within 4Å: Chain B: K.37, N.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.37 NAG.36: 4 residues within 4Å: Chain A: S.232 Chain B: N.180, N.251 Ligands: SO4.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.180, B:N.251 NAG.37: 6 residues within 4Å: Chain B: E.492, E.495, S.496, N.499, T.501 Ligands: SO4.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.492, B:E.495, B:T.501 NAG.38: 1 residues within 4Å: Chain B: N.169 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.169 NAG.54: 2 residues within 4Å: Chain C: K.37, N.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.37 NAG.55: 4 residues within 4Å: Chain B: S.232 Chain C: N.180, N.251 Ligands: SO4.50 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.180, C:N.251 NAG.56: 6 residues within 4Å: Chain C: E.492, E.495, S.496, N.499, T.501 Ligands: SO4.49 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.492, C:E.495, C:T.501 NAG.57: 1 residues within 4Å: Chain C: N.169 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antanasijevic, A. et al., Identification of a pH sensor in Influenza hemagglutinin using X-ray crystallography. J.Struct.Biol. (2020)

Release Date

2019-11-13

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Hemagglutinin

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