SMTL ID : 6hrr.2 (1 other biounit)

Structure of the TRPML2 ELD at pH 6.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: K.74, H.76, L.122, E.123, L.127 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: K.74, H.76, L.122, E.123, L.127 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain C: K.74, H.76, L.122, E.123, L.127 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain D: K.74, H.76, L.122, E.123, L.127 Ligand excluded by PLIP

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: H.12, L.13, F.42, Q.46, I.53 Chain D: T.32 Ligands: GOL.31 Ligand excluded by PLIP GOL.3: 4 residues within 4Å: Chain A: Q.33, E.34, Y.37 Chain C: D.52 Ligand excluded by PLIP GOL.4: 2 residues within 4Å: Chain A: D.35 Ligands: GOL.20 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: E.34, Y.37, F.41 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: G.17, Y.18, S.19, E.23, C.28, S.29 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: D.24, D.25 Ligands: MES.8 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain B: H.12, L.13, F.42, Q.46, I.53 Chain C: T.32 Ligands: GOL.22 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: Q.33, E.34, Y.37 Chain D: D.52 Ligand excluded by PLIP GOL.13: 2 residues within 4Å: Chain B: D.35 Ligands: GOL.29 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain B: E.34, Y.37, F.41 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: G.17, Y.18, S.19, E.23, C.28, S.29 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain B: D.24, D.25 Ligands: MES.17 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain A: T.32 Chain C: H.12, L.13, F.42, Q.46, I.53 Ligands: GOL.4 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: D.52 Chain C: Q.33, E.34, Y.37 Ligand excluded by PLIP GOL.22: 2 residues within 4Å: Chain C: D.35 Ligands: GOL.11 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain C: E.34, Y.37, F.41 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain C: G.17, Y.18, S.19, E.23, C.28, S.29 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain C: D.24, D.25 Ligands: MES.26 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain B: T.32 Chain D: H.12, L.13, F.42, Q.46, I.53 Ligands: GOL.13 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain A: D.52 Chain D: Q.33, E.34, Y.37 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain D: D.35 Ligands: GOL.2 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain D: E.34, Y.37, F.41 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain D: G.17, Y.18, S.19, E.23, C.28, S.29 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain D: D.24, D.25 Ligands: MES.35 Ligand excluded by PLIP

8 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.8: 9 residues within 4Å: Chain A: K.11, D.22, D.24, D.25, Y.26, S.27, Y.173, F.174 Ligands: GOL.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.27, A:S.27, A:S.27, A:F.174 Water bridges: A:K.11 Salt bridges: A:K.11, A:D.22 MES.9: 6 residues within 4Å: Chain A: H.76, K.78, K.79, E.96, D.98, R.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.79 Salt bridges: A:H.76, A:E.96, A:D.98, A:R.126 MES.17: 9 residues within 4Å: Chain B: K.11, D.22, D.24, D.25, Y.26, S.27, Y.173, F.174 Ligands: GOL.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.27, B:S.27, B:S.27, B:F.174 Water bridges: B:K.11 Salt bridges: B:K.11, B:D.22 MES.18: 6 residues within 4Å: Chain B: H.76, K.78, K.79, E.96, D.98, R.126 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.79 Salt bridges: B:H.76, B:E.96, B:D.98, B:R.126 MES.26: 9 residues within 4Å: Chain C: K.11, D.22, D.24, D.25, Y.26, S.27, Y.173, F.174 Ligands: GOL.25 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.27, C:S.27, C:S.27, C:F.174 Water bridges: C:K.11 Salt bridges: C:K.11, C:D.22 MES.27: 6 residues within 4Å: Chain C: H.76, K.78, K.79, E.96, D.98, R.126 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.79 Salt bridges: C:H.76, C:E.96, C:D.98, C:R.126 MES.35: 9 residues within 4Å: Chain D: K.11, D.22, D.24, D.25, Y.26, S.27, Y.173, F.174 Ligands: GOL.34 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.27, D:S.27, D:S.27, D:F.174 Water bridges: D:K.11 Salt bridges: D:K.11, D:D.22 MES.36: 6 residues within 4Å: Chain D: H.76, K.78, K.79, E.96, D.98, R.126 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.79 Salt bridges: D:H.76, D:E.96, D:D.98, D:R.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viet, K.K. et al., Structure of the Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain. Structure (2019)

Release Date

2019-06-19

Peptides

Mucolipin-2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Mucolipin-2

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