SMTL ID : 5iwp.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.65 Å

Oligo State

homo-tetramer

Ligands

12 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.5, CA.9, CA.13 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Metal complexes: A:D.541, C:D.541, B:D.541, D: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.3: 3 residues within 4Å: Ligands: CA.7, CA.11, CA.15 No protein-ligand interaction detected (PLIP) CA.5: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.1, CA.9, CA.13 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Metal complexes: A:D.541, C:D.541, B:D.541, D: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.7: 3 residues within 4Å: Ligands: CA.3, CA.11, CA.15 No protein-ligand interaction detected (PLIP) CA.9: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.1, CA.5, CA.13 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Metal complexes: A:D.541, C:D.541, B:D.541, D: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.11: 3 residues within 4Å: Ligands: CA.3, CA.7, CA.15 No protein-ligand interaction detected (PLIP) CA.13: 7 residues within 4Å: Chain A: D.541 Chain B: D.541 Chain C: D.541 Chain D: D.541 Ligands: CA.1, CA.5, CA.9 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Metal complexes: A:D.541, C:D.541, B:D.541, D: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) CA.15: 3 residues within 4Å: Ligands: CA.3, CA.7, CA.11 No protein-ligand interaction detected (PLIP)

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

DTB.4: 10 residues within 4Å: Chain A: Q.40, L.88, Y.115, V.151, L.159, I.160 Chain D: W.267, Y.269, L.272, E.633 15 PLIP interactions: 8 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:W.267, D:W.267, D:Y.269, D:Y.269, D:L.272, A:L.88, A:Y.115, A:I.160 Hydrogen bonds: D:E.633, A:Q.40, A:Q.40, A:L.159 pi-Stacking: D:W.267, D:W.267 Salt bridges: A:R.33 DTB.8: 10 residues within 4Å: Chain B: Q.40, L.88, Y.115, V.151, L.159, I.160 Chain C: W.267, Y.269, L.272, E.633 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:L.88, B:Y.115, B:I.160, C:W.267, C:W.267, C:Y.269, C:Y.269, C:L.272 Hydrogen bonds: B:Q.40, B:Q.40, B:L.159, C:E.633 Salt bridges: B:R.33 pi-Stacking: C:W.267, C:W.267 DTB.12: 10 residues within 4Å: Chain A: W.267, Y.269, L.272, E.633 Chain C: Q.40, L.88, Y.115, V.151, L.159, I.160 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:W.267, A:W.267, A:Y.269, A:Y.269, A:L.272, C:L.88, C:Y.115, C:I.160 Hydrogen bonds: A:E.633, C:Q.40, C:Q.40, C:L.159 pi-Stacking: A:W.267, A:W.267 Salt bridges: C:R.33 DTB.16: 10 residues within 4Å: Chain B: W.267, Y.269, L.272, E.633 Chain D: Q.40, L.88, Y.115, V.151, L.159, I.160 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:W.267, B:W.267, B:Y.269, B:Y.269, B:L.272, D:L.88, D:Y.115, D:I.160 Hydrogen bonds: B:E.633, D:Q.40, D:Q.40, D:L.159 pi-Stacking: B:W.267, 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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