SMTL ID : 6hdb.1

Crystal structure of the potassium channel MtTMEM175 with zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-4-4-mer

Ligands

4 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 19 residues within 4Å: Chain A: N.129, D.131, K.132, E.161, W.179, A.180, D.182, R.183, E.228, N.267, E.270, P.271, Y.272, F.273, W.347, G.377, M.447, W.457, R.461 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.179, A:D.182, A:R.183, A:R.183, A:E.270, A:E.270, A:Y.272, A:R.461 GLC-GLC.6: 19 residues within 4Å: Chain C: N.129, D.131, K.132, E.161, W.179, A.180, D.182, R.183, E.228, N.267, E.270, P.271, Y.272, F.273, W.347, G.377, M.447, W.457, R.461 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:W.179, C:D.182, C:R.183, C:R.183, C:E.270, C:E.270, C:Y.272, C:R.461 GLC-GLC.11: 19 residues within 4Å: Chain E: N.129, D.131, K.132, E.161, W.179, A.180, D.182, R.183, E.228, N.267, E.270, P.271, Y.272, F.273, W.347, G.377, M.447, W.457, R.461 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:W.179, E:D.182, E:R.183, E:R.183, E:E.270, E:E.270, E:Y.272, E:R.461 GLC-GLC.16: 19 residues within 4Å: Chain G: N.129, D.131, K.132, E.161, W.179, A.180, D.182, R.183, E.228, N.267, E.270, P.271, Y.272, F.273, W.347, G.377, M.447, W.457, R.461 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:W.179, G:D.182, G:R.183, G:R.183, G:E.270, G:E.270, G:Y.272, G:R.461

4 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.2: 18 residues within 4Å: Chain B: S.45, T.46, P.48, A.56, S.57, R.59, D.60, I.62, P.63, R.115, S.118, E.119, G.122, I.127, I.128, R.134, F.135 Chain H: E.49 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.62, B:E.119 Hydrogen bonds: B:T.46, B:T.46, B:E.119 Water bridges: B:S.45, B:K.111 Salt bridges: B:R.59, B:R.115, B:R.134 LMT.7: 18 residues within 4Å: Chain D: S.45, T.46, P.48, A.56, S.57, R.59, D.60, I.62, P.63, R.115, S.118, E.119, G.122, I.127, I.128, R.134, F.135 Chain F: E.49 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.62, D:E.119 Hydrogen bonds: D:T.46, D:T.46, D:E.119 Water bridges: D:S.45, D:K.111 Salt bridges: D:R.59, D:R.115, D:R.134 LMT.12: 18 residues within 4Å: Chain B: E.49 Chain F: S.45, T.46, P.48, A.56, S.57, R.59, D.60, I.62, P.63, R.115, S.118, E.119, G.122, I.127, I.128, R.134, F.135 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:I.62, F:E.119 Hydrogen bonds: F:T.46, F:T.46, F:E.119 Water bridges: F:S.45, F:K.111 Salt bridges: F:R.59, F:R.115, F:R.134 LMT.17: 18 residues within 4Å: Chain D: E.49 Chain H: S.45, T.46, P.48, A.56, S.57, R.59, D.60, I.62, P.63, R.115, S.118, E.119, G.122, I.127, I.128, R.134, F.135 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:I.62, H:E.119 Hydrogen bonds: H:T.46, H:T.46, H:E.119 Water bridges: H:S.45, H:K.111 Salt bridges: H:R.59, H:R.115, H:R.134

8 x K: POTASSIUM ION(Non-functional Binders)

K.3: 3 residues within 4Å: Ligands: K.8, K.13, K.18 No protein-ligand interaction detected (PLIP) K.4: 10 residues within 4Å: Chain B: T.28 Chain D: T.28, A.32 Chain F: T.28, A.32 Chain H: T.28, A.32 Ligands: K.9, K.14, K.19 No protein-ligand interaction detected (PLIP) K.8: 3 residues within 4Å: Ligands: K.3, K.13, K.18 No protein-ligand interaction detected (PLIP) K.9: 10 residues within 4Å: Chain B: T.28, A.32 Chain D: T.28 Chain F: T.28, A.32 Chain H: T.28, A.32 Ligands: K.4, K.14, K.19 No protein-ligand interaction detected (PLIP) K.13: 3 residues within 4Å: Ligands: K.3, K.8, K.18 No protein-ligand interaction detected (PLIP) K.14: 10 residues within 4Å: Chain B: T.28, A.32 Chain D: T.28, A.32 Chain F: T.28 Chain H: T.28, A.32 Ligands: K.4, K.9, K.19 No protein-ligand interaction detected (PLIP) K.18: 3 residues within 4Å: Ligands: K.3, K.8, K.13 No protein-ligand interaction detected (PLIP) K.19: 10 residues within 4Å: Chain B: T.28, A.32 Chain D: T.28, A.32 Chain F: T.28, A.32 Chain H: T.28 Ligands: K.4, K.9, K.14 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 11 residues within 4Å: Chain B: L.36, L.40 Chain D: L.36, L.40 Chain F: L.36, L.40 Chain H: L.36, L.40 Ligands: ZN.10, ZN.15, ZN.20 No protein-ligand interaction detected (PLIP) ZN.10: 11 residues within 4Å: Chain B: L.36, L.40 Chain D: L.36, L.40 Chain F: L.36, L.40 Chain H: L.36, L.40 Ligands: ZN.5, ZN.15, ZN.20 No protein-ligand interaction detected (PLIP) ZN.15: 11 residues within 4Å: Chain B: L.36, L.40 Chain D: L.36, L.40 Chain F: L.36, L.40 Chain H: L.36, L.40 Ligands: ZN.5, ZN.10, ZN.20 No protein-ligand interaction detected (PLIP) ZN.20: 11 residues within 4Å: Chain B: L.36, L.40 Chain D: L.36, L.40 Chain F: L.36, L.40 Chain H: L.36, L.40 Ligands: ZN.5, ZN.10, ZN.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brunner, J.D. et al., Structural basis for ion selectivity in TMEM175 K+channels. Elife (2020)

Release Date

2019-08-28

Peptides

Nanobody,Maltose/maltodextrin-binding periplasmic protein: ACEG
TMEM175: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

Membrane

We predict this structure to be a membrane protein.
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Nanobody,Maltose/maltodextrin-binding periplasmic protein

TMEM175

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