SMTL ID : 4qkc.1

Influenza A M2 wild type TM domain at low pH in the lipidic cubic phase under cryo diffraction conditions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 10 residues within 4Å: Chain A: S.2, S.3 Chain B: S.2, S.3 Chain C: S.2 Chain D: S.2, S.3 Ligands: CA.7, CA.13, CA.19 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:S.2, A:S.2, D:S.2, H2O.2, H2O.5 CA.3: 2 residues within 4Å: Chain A: D.4 Ligands: OLB.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.4, H2O.1, H2O.1, H2O.1, H2O.4 CA.7: 10 residues within 4Å: Chain A: S.2, S.3 Chain B: S.2, S.3 Chain C: S.2, S.3 Chain D: S.2 Ligands: CA.1, CA.13, CA.19 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:S.2, A:S.2, C:S.2, H2O.4, H2O.7 CA.9: 2 residues within 4Å: Chain B: D.4 Ligands: OLB.11 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.4, H2O.3, H2O.3, H2O.3, H2O.6 CA.13: 10 residues within 4Å: Chain A: S.2, S.3 Chain B: S.2 Chain C: S.2, S.3 Chain D: S.2, S.3 Ligands: CA.1, CA.7, CA.19 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:S.2, D:S.2, C:S.2, H2O.4, H2O.5 CA.15: 2 residues within 4Å: Chain C: D.4 Ligands: OLB.17 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.4, H2O.2, H2O.4, H2O.4, H2O.4 CA.19: 10 residues within 4Å: Chain A: S.2 Chain B: S.2, S.3 Chain C: S.2, S.3 Chain D: S.2, S.3 Ligands: CA.1, CA.7, CA.13 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:S.2, B:S.2, D:S.2, H2O.2, H2O.7 CA.21: 2 residues within 4Å: Chain D: D.4 Ligands: OLB.23 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.4, H2O.1, H2O.6, H2O.6, H2O.6

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 11 residues within 4Å: Chain A: S.3, V.7 Chain B: S.3, V.7 Chain C: S.3, V.7 Chain D: S.3, V.7 Ligands: CL.8, CL.14, CL.20 Ligand excluded by PLIP CL.8: 11 residues within 4Å: Chain A: S.3, V.7 Chain B: S.3, V.7 Chain C: S.3, V.7 Chain D: S.3, V.7 Ligands: CL.2, CL.14, CL.20 Ligand excluded by PLIP CL.14: 11 residues within 4Å: Chain A: S.3, V.7 Chain B: S.3, V.7 Chain C: S.3, V.7 Chain D: S.3, V.7 Ligands: CL.2, CL.8, CL.20 Ligand excluded by PLIP CL.20: 11 residues within 4Å: Chain A: S.3, V.7 Chain B: S.3, V.7 Chain C: S.3, V.7 Chain D: S.3, V.7 Ligands: CL.2, CL.8, CL.14 Ligand excluded by PLIP

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

EDO.4: 6 residues within 4Å: Chain A: H.17, L.18, W.21 Chain D: H.17 Ligands: EDO.16, EDO.22 1 PLIP interactions: 1 interactions with chain D Water bridges: D:H.17 EDO.10: 6 residues within 4Å: Chain B: H.17, L.18, W.21 Chain C: H.17 Ligands: EDO.16, EDO.22 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.17 EDO.16: 6 residues within 4Å: Chain A: H.17 Chain C: H.17, L.18, W.21 Ligands: EDO.4, EDO.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.17 EDO.22: 6 residues within 4Å: Chain B: H.17 Chain D: H.17, L.18, W.21 Ligands: EDO.4, EDO.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.17

8 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.5: 12 residues within 4Å: Chain A: D.4, P.5, L.6, A.9, I.13 Chain C: X.1, I.15, L.18, I.19, I.22 Ligands: CA.3, OLB.6 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.6, A:A.9, C:I.15, C:L.18, C:I.19, C:I.22 Hydrogen bonds: A:D.4 OLB.6: 12 residues within 4Å: Chain A: P.5, V.8, A.9, I.12, I.13, L.16, H.17, L.20 Chain C: L.18, W.21, I.22 Ligands: OLB.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.12, A:I.13, A:H.17, A:L.20 OLB.11: 12 residues within 4Å: Chain B: D.4, P.5, L.6, A.9, I.13 Chain D: X.1, I.15, L.18, I.19, I.22 Ligands: CA.9, OLB.12 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:L.6, B:A.9, D:I.15, D:L.18, D:I.19, D:I.22 Hydrogen bonds: B:D.4 OLB.12: 12 residues within 4Å: Chain B: P.5, V.8, A.9, I.12, I.13, L.16, H.17, L.20 Chain D: L.18, W.21, I.22 Ligands: OLB.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.12, B:I.13, B:H.17, B:L.20 OLB.17: 12 residues within 4Å: Chain B: X.1, I.15, L.18, I.19, I.22 Chain C: D.4, P.5, L.6, A.9, I.13 Ligands: CA.15, OLB.18 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:I.15, B:L.18, B:I.19, B:I.22, C:L.6, C:A.9 Hydrogen bonds: C:D.4, C:D.4 OLB.18: 12 residues within 4Å: Chain B: L.18, W.21, I.22 Chain C: P.5, V.8, A.9, I.12, I.13, L.16, H.17, L.20 Ligands: OLB.17 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.12, C:I.13, C:H.17, C:L.20 OLB.23: 12 residues within 4Å: Chain A: X.1, I.15, L.18, I.19, I.22 Chain D: D.4, P.5, L.6, A.9, I.13 Ligands: CA.21, OLB.24 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:I.15, A:L.18, A:I.19, A:I.22, D:L.6, D:A.9 Hydrogen bonds: D:D.4 OLB.24: 12 residues within 4Å: Chain A: L.18, W.21, I.22 Chain D: P.5, V.8, A.9, I.12, I.13, L.16, H.17, L.20 Ligands: OLB.23 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.12, D:I.13, D:H.17, D:L.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomaston, J.L. et al., High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-11-11

Peptides

influenza M2 monomer: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Membrane

We predict this structure to be a membrane protein.
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influenza M2 monomer

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