SMTL ID : 6pd6.1

Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 7.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: W.75, G.78, I.86, K.128, N.161, Y.269 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: S.147, S.148, Q.237 Ligands: SO4.7 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: 8 residues within 4Å: Chain A: G.315, E.316, C.317, K.319, T.406, Q.407, E.409 Chain C: D.435 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain A: L.144, G.145, V.146, W.164, L.205 Ligands: SO4.2 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: P.173, T.174 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Ligands: NAG.13 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain A: M.447 Chain B: M.447 Chain C: M.447 Ligands: SO4.33, SO4.51 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain A: E.492 Ligands: NAG.18 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain B: W.75, G.78, I.86, K.128, N.161, Y.269 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: S.147, S.148, Q.237 Ligands: SO4.25 Ligand excluded by PLIP SO4.21: 6 residues within 4Å: Chain B: S.136, W.137, S.138, S.139, H.140, R.177 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain B: D.198, A.199 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: Q.130, P.133, K.134, S.135 Ligand excluded by PLIP SO4.24: 8 residues within 4Å: Chain A: D.435 Chain B: G.315, E.316, C.317, K.319, T.406, Q.407, E.409 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain B: L.144, G.145, V.146, W.164, L.205 Ligands: SO4.20 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: P.173, T.174 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Ligands: NAG.31 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain A: M.447 Chain B: M.447 Chain C: M.447 Ligands: SO4.15, SO4.51 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain B: E.492 Ligands: NAG.36 Ligand excluded by PLIP SO4.37: 6 residues within 4Å: Chain C: W.75, G.78, I.86, K.128, N.161, Y.269 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain C: S.147, S.148, Q.237 Ligands: SO4.43 Ligand excluded by PLIP SO4.39: 6 residues within 4Å: Chain C: S.136, W.137, S.138, S.139, H.140, R.177 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain C: D.198, A.199 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain C: Q.130, P.133, K.134, S.135 Ligand excluded by PLIP SO4.42: 8 residues within 4Å: Chain B: D.435 Chain C: G.315, E.316, C.317, K.319, T.406, Q.407, E.409 Ligand excluded by PLIP SO4.43: 6 residues within 4Å: Chain C: L.144, G.145, V.146, W.164, L.205 Ligands: SO4.38 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain C: P.173, T.174 Ligand excluded by PLIP SO4.45: 1 residues within 4Å: Ligands: NAG.49 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain A: M.447 Chain B: M.447 Chain C: M.447 Ligands: SO4.15, SO4.33 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain C: E.492 Ligands: NAG.54 Ligand excluded by PLIP

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: H.43, Q.45, T.330, W.366, V.393, T.394 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.43 GOL.11: 3 residues within 4Å: Chain A: D.103, F.110, Y.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.110, A:F.110 Water bridges: A:D.103, A:Y.113 GOL.17: 7 residues within 4Å: Chain A: A.381, D.382, K.383, E.384, E.495, R.498, N.499 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.382, A:E.384, A:E.495 GOL.28: 6 residues within 4Å: Chain B: H.43, Q.45, T.330, W.366, V.393, T.394 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.43 GOL.29: 3 residues within 4Å: Chain B: D.103, F.110, Y.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.110, B:F.110 Water bridges: B:D.103, B:Y.113 GOL.35: 7 residues within 4Å: Chain B: A.381, D.382, K.383, E.384, E.495, R.498, N.499 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.382, B:E.384, B:E.495 GOL.46: 6 residues within 4Å: Chain C: H.43, Q.45, T.330, W.366, V.393, T.394 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.43 GOL.47: 3 residues within 4Å: Chain C: D.103, F.110, Y.113 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.110, C:F.110 Water bridges: C:D.103, C:Y.113 GOL.53: 7 residues within 4Å: Chain C: A.381, D.382, K.383, E.384, E.495, R.498, N.499 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.382, C:E.384, C:E.495

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

NAG.12: 1 residues within 4Å: Chain A: N.38 No protein-ligand interaction detected (PLIP) NAG.13: 6 residues within 4Å: Chain A: N.180, N.251, D.252, A.253 Chain C: S.232 Ligands: SO4.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.180 NAG.14: 1 residues within 4Å: Chain A: N.169 No protein-ligand interaction detected (PLIP) NAG.18: 5 residues within 4Å: Chain A: E.492, E.495, N.499, T.501 Ligands: SO4.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.492, A:N.499, A:T.501, A:T.501 NAG.30: 1 residues within 4Å: Chain B: N.38 No protein-ligand interaction detected (PLIP) NAG.31: 6 residues within 4Å: Chain A: S.232 Chain B: N.180, N.251, D.252, A.253 Ligands: SO4.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.180 NAG.32: 1 residues within 4Å: Chain B: N.169 No protein-ligand interaction detected (PLIP) NAG.36: 5 residues within 4Å: Chain B: E.492, E.495, N.499, T.501 Ligands: SO4.34 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.492, B:N.499, B:T.501, B:T.501 NAG.48: 1 residues within 4Å: Chain C: N.38 No protein-ligand interaction detected (PLIP) NAG.49: 6 residues within 4Å: Chain B: S.232 Chain C: N.180, N.251, D.252, A.253 Ligands: SO4.45 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.180 NAG.50: 1 residues within 4Å: Chain C: N.169 No protein-ligand interaction detected (PLIP) NAG.54: 5 residues within 4Å: Chain C: E.492, E.495, N.499, T.501 Ligands: SO4.52 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.492, C:N.499, C:T.501, C:T.501

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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