SMTL ID : 6d7q.1

Crystal Structure of Rat TRPV6*-Y466A in complex with 2-Aminoethoxydiphenyl borate (2-APB)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-tetramer

Ligands

4 x FZ4: 2-aminoethyl diphenylborinate(Non-covalent)

FZ4.1: 10 residues within 4Å: Chain A: F.328, E.402, G.421, G.422, H.425, R.469, A.598, T.599, M.602, L.603 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.328, A:A.598, A:T.599, A:L.603 Hydrogen bonds: A:E.402 FZ4.4: 10 residues within 4Å: Chain B: F.328, E.402, G.421, G.422, H.425, R.469, A.598, T.599, M.602, L.603 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.328, B:A.598, B:T.599, B:L.603 Hydrogen bonds: B:E.402 FZ4.7: 10 residues within 4Å: Chain C: F.328, E.402, G.421, G.422, H.425, R.469, A.598, T.599, M.602, L.603 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.328, C:A.598, C:T.599, C:L.603 Hydrogen bonds: C:E.402 FZ4.10: 10 residues within 4Å: Chain D: F.328, E.402, G.421, G.422, H.425, R.469, A.598, T.599, M.602, L.603 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.328, D:A.598, D:T.599, D:L.603 Hydrogen bonds: D:E.402

4 x DTB: 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID(Non-covalent)

DTB.2: 12 residues within 4Å: Chain A: R.33, Q.40, M.78, I.85, L.88, M.110, Y.115, V.151 Chain D: W.267, Y.269, L.272, E.633 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:Y.115, A:Y.115, D:W.267, D:Y.269, D:Y.269, D:Y.269 Hydrogen bonds: A:Q.40 Salt bridges: A:R.33 pi-Stacking: A:Y.115 DTB.5: 12 residues within 4Å: Chain B: R.33, Q.40, M.78, I.85, L.88, M.110, Y.115, V.151 Chain C: W.267, Y.269, L.272, E.633 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.115, B:Y.115, C:W.267, C:Y.269, C:Y.269, C:Y.269 Hydrogen bonds: B:Q.40 Salt bridges: B:R.33 pi-Stacking: B:Y.115 DTB.8: 12 residues within 4Å: Chain A: W.267, Y.269, L.272, E.633 Chain C: R.33, Q.40, M.78, I.85, L.88, M.110, Y.115, V.151 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:Y.115, C:Y.115, A:W.267, A:Y.269, A:Y.269, A:Y.269 Hydrogen bonds: C:Q.40 Salt bridges: C:R.33 pi-Stacking: C:Y.115 DTB.11: 12 residues within 4Å: Chain B: W.267, Y.269, L.272, E.633 Chain D: R.33, Q.40, M.78, I.85, L.88, M.110, Y.115, V.151 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:W.267, B:Y.269, B:Y.269, B:Y.269, D:Y.115, D:Y.115 Hydrogen bonds: D:Q.40 Salt bridges: D:R.33 pi-Stacking: D:Y.115

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.6, CA.9, CA.12 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Metal complexes: B:D.541, A:D.541, C:D.541, C:D.541, D:D.541 CA.6: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.3, CA.9, CA.12 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 2 interactions with chain D Metal complexes: B:D.541, A:D.541, C:D.541, D:D.541, D:D.541 CA.9: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.3, CA.6, CA.12 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain D Metal complexes: B:D.541, B:D.541, C:D.541, C:D.541, D:D.541 CA.12: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.3, CA.6, CA.9 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 interactions with chain D Metal complexes: A:D.541, A:D.541, C:D.541, D:D.541, D:D.541

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., Structural bases of TRP channel TRPV6 allosteric modulation by 2-APB. Nat Commun (2018)

Release Date

2018-07-18

Peptides

Transient receptor potential cation channel subfamily V member 6: 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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Transient receptor potential cation channel subfamily V member 6

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