SMTL ID : 7t3r.1

IP3 and ATP bound type 3 IP3 receptor in the pre-active C state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.2538, C.2541, H.2558, H.2563 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.2538, A:C.2541, A:H.2558, A:H.2563 ZN.4: 4 residues within 4Å: Chain B: C.2538, C.2541, H.2558, H.2563 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.2538, B:C.2541, B:H.2558, B:H.2563 ZN.7: 4 residues within 4Å: Chain C: C.2538, C.2541, H.2558, H.2563 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.2538, C:C.2541, C:H.2558, C:H.2563 ZN.10: 4 residues within 4Å: Chain D: C.2538, C.2541, H.2558, H.2563 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.2538, D:C.2541, D:H.2558, D:H.2563

4 x I3P: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE(Non-covalent)

I3P.2: 10 residues within 4Å: Chain A: R.266, T.268, L.269, R.270, R.411, K.507, R.510, Y.567, R.568, K.569 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.268, A:L.269, A:R.270, A:R.270, A:Y.567, A:R.568 Salt bridges: A:R.266, A:R.270, A:K.507, A:R.510, A:R.568, A:K.569, A:K.569 I3P.5: 10 residues within 4Å: Chain B: R.266, T.268, L.269, R.270, R.411, K.507, R.510, Y.567, R.568, K.569 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.268, B:L.269, B:R.270, B:R.270, B:R.411, B:Y.567, B:R.568 Salt bridges: B:R.266, B:R.270, B:K.507, B:R.510, B:R.568, B:K.569, B:K.569 I3P.8: 10 residues within 4Å: Chain C: R.266, T.268, L.269, R.270, R.411, K.507, R.510, Y.567, R.568, K.569 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.268, C:L.269, C:R.270, C:R.270, C:R.411, C:Y.567, C:R.568 Salt bridges: C:R.266, C:R.270, C:K.507, C:R.510, C:R.568, C:K.569, C:K.569 I3P.11: 10 residues within 4Å: Chain D: R.266, T.268, L.269, R.270, R.411, K.507, R.510, Y.567, R.568, K.569 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.268, D:L.269, D:R.270, D:R.270, D:R.411, D:Y.567, D:R.568 Salt bridges: D:R.266, D:R.270, D:K.507, D:R.510, D:R.568, D:K.569, D:K.569

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 12 residues within 4Å: Chain A: E.2149, K.2152, F.2156, C.2538, F.2539, I.2540, I.2559, K.2560, H.2563, N.2564, M.2565, W.2566 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.2149, A:F.2539, A:H.2563, A:N.2564, A:M.2565 Salt bridges: A:K.2152, A:K.2152, A:K.2560, A:K.2560, A:K.2560 ATP.6: 12 residues within 4Å: Chain B: E.2149, K.2152, F.2156, C.2538, F.2539, I.2540, I.2559, K.2560, H.2563, N.2564, M.2565, W.2566 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.2149, B:F.2539, B:H.2563, B:N.2564, B:M.2565 Salt bridges: B:K.2152, B:K.2152, B:K.2560, B:K.2560, B:K.2560 ATP.9: 12 residues within 4Å: Chain C: E.2149, K.2152, F.2156, C.2538, F.2539, I.2540, I.2559, K.2560, H.2563, N.2564, M.2565, W.2566 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:E.2149, C:F.2539, C:H.2563, C:N.2564, C:M.2565 Salt bridges: C:K.2152, C:K.2152, C:K.2560, C:K.2560, C:K.2560 ATP.12: 12 residues within 4Å: Chain D: E.2149, K.2152, F.2156, C.2538, F.2539, I.2540, I.2559, K.2560, H.2563, N.2564, M.2565, W.2566 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.2149, D:F.2539, D:H.2563, D:N.2564, D:M.2565 Salt bridges: D:K.2152, D:K.2152, D:K.2560, D:K.2560, D:K.2560

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmitz, E.A. et al., Structural basis for activation and gating of IP 3 receptors. Nat Commun (2022)

Release Date

2022-03-23

Peptides

Inositol 1,4,5-trisphosphate receptor type 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Inositol 1,4,5-trisphosphate receptor type 3

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