SMTL ID : 6d7o.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.45 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.4, CA.7, CA.10 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Metal complexes: B:D.541, A:D.541, C:D.541, D:D.541 CA.4: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.1, CA.7, CA.10 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Metal complexes: B:D.541, A:D.541, C:D.541, D:D.541 CA.7: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.1, CA.4, CA.10 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Metal complexes: B:D.541, A:D.541, C:D.541, D:D.541 CA.10: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.1, CA.4, CA.7 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Metal complexes: B:D.541, A:D.541, C:D.541, D:D.541

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

FZ4.2: 10 residues within 4Å: Chain A: V.401, E.402, G.422, F.424, H.425, I.428, N.463, Y.466, R.469, M.602 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.425, A:I.428 Hydrogen bonds: A:H.425 pi-Stacking: A:Y.466 pi-Cation interactions: A:R.469 FZ4.5: 10 residues within 4Å: Chain B: V.401, E.402, G.422, F.424, H.425, I.428, N.463, Y.466, R.469, M.602 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.425, B:I.428 Hydrogen bonds: B:H.425 pi-Stacking: B:Y.466 pi-Cation interactions: B:R.469 FZ4.8: 10 residues within 4Å: Chain C: V.401, E.402, G.422, F.424, H.425, I.428, N.463, Y.466, R.469, M.602 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:H.425, C:I.428 Hydrogen bonds: C:H.425 pi-Stacking: C:Y.466 pi-Cation interactions: C:R.469 FZ4.11: 10 residues within 4Å: Chain D: V.401, E.402, G.422, F.424, H.425, I.428, N.463, Y.466, R.469, M.602 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:H.425, D:I.428 Hydrogen bonds: D:H.425 pi-Stacking: D:Y.466 pi-Cation interactions: D:R.469

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

DTB.3: 12 residues within 4Å: Chain A: R.33, Q.40, L.88, M.110, Y.115, I.123, V.151, I.160 Chain D: W.267, Y.269, L.272, E.633 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:V.151, D:W.267, D:W.267, D:Y.269, D:Y.269, D:L.272 Hydrogen bonds: A:Q.40 Salt bridges: A:R.33 DTB.6: 12 residues within 4Å: Chain B: R.33, Q.40, L.88, M.110, Y.115, I.123, V.151, I.160 Chain C: W.267, Y.269, L.272, E.633 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.267, C:W.267, C:Y.269, C:Y.269, C:L.272, B:V.151 Hydrogen bonds: B:Q.40 Salt bridges: B:R.33 DTB.9: 12 residues within 4Å: Chain A: W.267, Y.269, L.272, E.633 Chain C: R.33, Q.40, L.88, M.110, Y.115, I.123, V.151, I.160 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:V.151, A:W.267, A:W.267, A:Y.269, A:Y.269, A:L.272 Hydrogen bonds: C:Q.40 Salt bridges: C:R.33 DTB.12: 12 residues within 4Å: Chain B: W.267, Y.269, L.272, E.633 Chain D: R.33, Q.40, L.88, M.110, Y.115, I.123, V.151, I.160 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:V.151, B:W.267, B:W.267, B:Y.269, B:Y.269, B:L.272 Hydrogen bonds: D:Q.40 Salt bridges: D:R.33

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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