SMTL ID : 6d7x.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 11 residues within 4Å: Chain A: I.539, D.541 Chain B: I.539, D.541 Chain C: I.539, D.541 Chain D: I.539, D.541 Ligands: CA.5, CA.9, CA.13 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:D.541, D:D.541, C:D.541, B:D.541 CA.2: 7 residues within 4Å: Chain A: T.538 Chain B: T.538 Chain C: T.538 Chain D: T.538 Ligands: CA.6, CA.10, CA.14 No protein-ligand interaction detected (PLIP) CA.5: 11 residues within 4Å: Chain A: I.539, D.541 Chain B: I.539, D.541 Chain C: I.539, D.541 Chain D: I.539, D.541 Ligands: CA.1, CA.9, CA.13 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:D.541, D:D.541, C:D.541, B:D.541 CA.6: 7 residues within 4Å: Chain A: T.538 Chain B: T.538 Chain C: T.538 Chain D: T.538 Ligands: CA.2, CA.10, CA.14 No protein-ligand interaction detected (PLIP) CA.9: 11 residues within 4Å: Chain A: I.539, D.541 Chain B: I.539, D.541 Chain C: I.539, D.541 Chain D: I.539, D.541 Ligands: CA.1, CA.5, CA.13 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:D.541, D:D.541, C:D.541, B:D.541 CA.10: 7 residues within 4Å: Chain A: T.538 Chain B: T.538 Chain C: T.538 Chain D: T.538 Ligands: CA.2, CA.6, CA.14 No protein-ligand interaction detected (PLIP) CA.13: 11 residues within 4Å: Chain A: I.539, D.541 Chain B: I.539, D.541 Chain C: I.539, D.541 Chain D: I.539, D.541 Ligands: CA.1, CA.5, CA.9 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:D.541, D:D.541, C:D.541, B:D.541 CA.14: 7 residues within 4Å: Chain A: T.538 Chain B: T.538 Chain C: T.538 Chain D: T.538 Ligands: CA.2, CA.6, CA.10 No protein-ligand interaction detected (PLIP)

4 x FYY: 2-aminoethyl (4-bromophenyl)phenylborinate(Covalent)

FYY.3: 11 residues within 4Å: Chain A: V.296, F.328, E.402, G.421, G.422, H.425, R.469, A.598, T.599, M.602, L.603 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.328, A:T.599, A:M.602, A:L.603 Hydrogen bonds: A:E.402, A:H.425 Halogen bonds: A:V.296 FYY.7: 11 residues within 4Å: Chain B: V.296, F.328, E.402, G.421, G.422, H.425, R.469, A.598, T.599, M.602, L.603 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.328, B:T.599, B:M.602, B:L.603 Hydrogen bonds: B:E.402, B:H.425 Halogen bonds: B:V.296 FYY.11: 11 residues within 4Å: Chain C: V.296, F.328, E.402, G.421, G.422, H.425, R.469, A.598, T.599, M.602, L.603 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.328, C:T.599, C:M.602, C:L.603 Hydrogen bonds: C:E.402, C:H.425 Halogen bonds: C:V.296 FYY.15: 11 residues within 4Å: Chain D: V.296, F.328, E.402, G.421, G.422, H.425, R.469, A.598, T.599, M.602, L.603 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.328, D:T.599, D:M.602, D:L.603 Hydrogen bonds: D:E.402, D:H.425 Halogen bonds: D:V.296

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

DTB.4: 13 residues within 4Å: Chain A: R.33, Q.40, M.78, H.84, L.88, Y.115, I.123, V.151, N.158, I.160 Chain D: W.267, Y.269, L.272 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:M.78, A:Y.115, A:Y.115, A:V.151, D:W.267, D:Y.269, D:Y.269, D:L.272 Hydrogen bonds: A:R.33, A:Q.40 pi-Stacking: D:W.267 DTB.8: 13 residues within 4Å: Chain B: R.33, Q.40, M.78, H.84, L.88, Y.115, I.123, V.151, N.158, I.160 Chain C: W.267, Y.269, L.272 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:W.267, C:Y.269, C:Y.269, C:L.272, B:M.78, B:Y.115, B:Y.115, B:V.151 pi-Stacking: C:W.267 Hydrogen bonds: B:R.33, B:Q.40 DTB.12: 13 residues within 4Å: Chain A: W.267, Y.269, L.272 Chain C: R.33, Q.40, M.78, H.84, L.88, Y.115, I.123, V.151, N.158, I.160 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:M.78, C:Y.115, C:Y.115, C:V.151, A:W.267, A:Y.269, A:Y.269, A:L.272 Hydrogen bonds: C:R.33, C:Q.40 pi-Stacking: A:W.267 DTB.16: 13 residues within 4Å: Chain B: W.267, Y.269, L.272 Chain D: R.33, Q.40, M.78, H.84, L.88, Y.115, I.123, V.151, N.158, I.160 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:M.78, D:Y.115, D:Y.115, D:V.151, B:W.267, B:Y.269, B:Y.269, B:L.272 Hydrogen bonds: D:R.33, D:Q.40 pi-Stacking: B:W.267

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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