SMTL ID : 4qk7.1

Influenza A M2 wild type TM domain at high 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: 11 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, S.3 Ligands: CA.7, CA.13, CA.19 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:S.2, A:S.2, H2O.2, H2O.3, H2O.4 CA.3: 3 residues within 4Å: Chain A: D.4, P.5 Ligands: OLB.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.4, H2O.1, H2O.1, H2O.1 CA.7: 11 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, S.3 Ligands: CA.1, CA.13, CA.19 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: D:S.2, B:S.2, H2O.2, H2O.3, H2O.5 CA.9: 3 residues within 4Å: Chain B: D.4, P.5 Ligands: OLB.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.4, H2O.2, H2O.2, H2O.2 CA.13: 11 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, S.3 Ligands: CA.1, CA.7, CA.19 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:S.2, C:S.2, H2O.3, H2O.4, H2O.5 CA.15: 3 residues within 4Å: Chain C: D.4, P.5 Ligands: OLB.17 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.4, H2O.3, H2O.3, H2O.3 CA.19: 11 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, S.3 Ligands: CA.1, CA.7, CA.13 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: D:S.2, A:S.2, H2O.2, H2O.4, H2O.5 CA.21: 3 residues within 4Å: Chain D: D.4, P.5 Ligands: OLB.23 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.4, H2O.4, H2O.5, H2O.5

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: 5 residues within 4Å: Chain A: L.18, W.21 Chain C: H.17 Ligands: EDO.16, EDO.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.17 EDO.10: 5 residues within 4Å: Chain B: L.18, W.21 Chain D: H.17 Ligands: EDO.16, EDO.22 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.17 EDO.16: 5 residues within 4Å: Chain B: H.17 Chain C: L.18, W.21 Ligands: EDO.4, EDO.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.17 EDO.22: 5 residues within 4Å: Chain A: H.17 Chain D: L.18, W.21 Ligands: EDO.4, EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.17

8 x OLB: (2S)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE(Non-covalent)

OLB.5: 11 residues within 4Å: Chain A: D.4, P.5, L.6, A.9, I.13 Chain D: I.15, L.18, I.19, I.22 Ligands: CA.3, OLB.6 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:I.15, D:L.18, D:I.22, A:P.5, A:L.6, A:A.9 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 D: L.18, W.21, I.22 Ligands: OLB.5 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.8, A:A.9, A:I.12, A:I.13, A:I.13, A:L.16, A:L.16, A:H.17, A:L.20, D:L.18 OLB.11: 11 residues within 4Å: Chain B: D.4, P.5, L.6, A.9, I.13 Chain C: I.15, L.18, I.19, I.22 Ligands: CA.9, OLB.12 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.15, C:L.18, C:I.22, B:P.5, B:L.6, B:A.9 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 C: L.18, W.21, I.22 Ligands: OLB.11 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.8, B:A.9, B:I.12, B:I.13, B:I.13, B:L.16, B:L.16, B:H.17, B:L.20, C:L.18 OLB.17: 11 residues within 4Å: Chain A: 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 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:P.5, C:L.6, C:A.9, A:I.15, A:L.18, A:I.22 OLB.18: 12 residues within 4Å: Chain A: 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 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.8, C:A.9, C:I.12, C:I.13, C:I.13, C:L.16, C:L.16, C:H.17, C:L.20, A:L.18 OLB.23: 11 residues within 4Å: Chain B: 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 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:I.15, B:L.18, B:I.22, D:P.5, D:L.6, D:A.9 OLB.24: 12 residues within 4Å: Chain B: 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 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:V.8, D:A.9, D:I.12, D:I.13, D:I.13, D:L.16, D:L.16, D:H.17, D:L.20, B:L.18

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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