SMTL ID : 7t3u.1

IP3, ATP, and Ca2+ bound type 3 IP3 receptor in the inactive 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.5: 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.8: 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.11: 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

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

I3P.2: 5 residues within 4Å: Chain A: T.268, L.269, R.270, R.568, K.569 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.269, A:R.270 I3P.12: 5 residues within 4Å: Chain D: T.268, L.269, R.270, R.568, K.569 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.269, D:R.270, D:K.569

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

ATP.3: 10 residues within 4Å: Chain A: K.2152, 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:F.2539, A:I.2540, 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: 10 residues within 4Å: Chain B: K.2152, 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:F.2539, B:I.2540, 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: 11 residues within 4Å: Chain C: 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:F.2539, C:I.2540, 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.13: 11 residues within 4Å: Chain D: 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:F.2539, D:I.2540, 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

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.1882, E.1946, T.2581, Y.2583 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.1882, A:E.1946, A:T.2581 CA.7: 3 residues within 4Å: Chain B: E.1882, E.1946, T.2581 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.1882, B:E.1946, B:E.1946, B:T.2581 CA.10: 6 residues within 4Å: Chain C: E.1882, H.1884, E.1946, Q.1949, T.2581, Y.2583 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.1946, C:E.1946, C:T.2581 CA.14: 5 residues within 4Å: Chain D: E.1882, H.1884, E.1946, T.2581, Y.2583 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.1882, D:E.1946, D:T.2581

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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