SMTL ID : 5iwt.1

Structure of Transient Receptor Potential (TRP) channel TRPV6 in the presence of gadolinium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

homo-tetramer

Ligands

8 x GD: GADOLINIUM ATOM(Non-covalent)(Non-functional Binders)

GD.1: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: GD.4, GD.7, GD.10 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: D:D.541, C:D.541, B:D.541, A:D.541 GD.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GD.4: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: GD.1, GD.7, GD.10 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: D:D.541, C:D.541, B:D.541, A:D.541 GD.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GD.7: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: GD.1, GD.4, GD.10 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: D:D.541, C:D.541, B:D.541, A:D.541 GD.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GD.10: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: GD.1, GD.4, GD.7 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: D:D.541, C:D.541, B:D.541, A:D.541 GD.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

DTB.3: 13 residues within 4Å: Chain A: R.33, Q.40, L.88, M.110, Y.115, Q.118, V.151, F.152, N.158 Chain D: W.267, Y.269, L.272, E.633 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain D Hydrophobic interactions: A:L.88, A:Y.115, D:W.267, D:W.267, D:Y.269, D:Y.269, D:Y.269, D:L.272 Hydrogen bonds: A:Q.40, A:Q.40, A:Q.118, D:E.633 Salt bridges: A:R.33 pi-Stacking: D:W.267 DTB.6: 13 residues within 4Å: Chain B: R.33, Q.40, L.88, M.110, Y.115, Q.118, V.151, F.152, N.158 Chain C: W.267, Y.269, L.272, E.633 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:W.267, C:W.267, C:Y.269, C:Y.269, C:Y.269, C:L.272, B:L.88, B:Y.115 Hydrogen bonds: C:E.633, B:Q.40, B:Q.40, B:Q.118 pi-Stacking: C:W.267 Salt bridges: B:R.33 DTB.9: 13 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, Q.118, V.151, F.152, N.158 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:W.267, A:W.267, A:Y.269, A:Y.269, A:Y.269, A:L.272, C:L.88, C:Y.115 Hydrogen bonds: A:E.633, C:Q.40, C:Q.40, C:Q.118 pi-Stacking: A:W.267 Salt bridges: C:R.33 DTB.12: 13 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, Q.118, V.151, F.152, N.158 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:W.267, B:W.267, B:Y.269, B:Y.269, B:Y.269, B:L.272, D:L.88, D:Y.115 Hydrogen bonds: B:E.633, D:Q.40, D:Q.40, D:Q.118 pi-Stacking: B:W.267 Salt bridges: D:R.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saotome, K. et al., Crystal structure of the epithelial calcium channel TRPV6. Nature (2016)

Release Date

2016-06-15

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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