SMTL ID : 8tla.1

Human Type 3 IP3 Receptor - Higher-Order Inhibited State - Symmetry Mate 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.2538, I.2540, 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.9: 5 residues within 4Å: Chain C: C.2538, I.2540, 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.13: 5 residues within 4Å: Chain D: C.2538, I.2540, 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: 9 residues within 4Å: Chain A: R.266, T.268, L.269, R.270, K.507, R.510, Y.567, R.568, K.569 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:L.269, A:R.270, A:Y.567, A:R.568 Salt bridges: A:R.266, A:R.270, A:R.270, A:K.507, A:R.568, A:K.569 I3P.6: 8 residues within 4Å: Chain B: R.266, R.270, R.503, K.507, R.510, Y.567, R.568, K.569 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.567, B:R.568, B:K.569 Salt bridges: B:R.266, B:R.270, B:R.270, B:K.507, B:R.510, B:R.568, B:K.569, B:K.569 I3P.10: 7 residues within 4Å: Chain C: R.270, R.503, K.507, R.510, Y.567, R.568, K.569 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.503, C:R.510, C:Y.567, C:R.568 Salt bridges: C:R.270, C:R.270, C:K.507, C:K.569, C:K.569 I3P.14: 10 residues within 4Å: Chain D: R.266, T.268, L.269, R.270, R.503, K.507, R.510, Y.567, R.568, K.569 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.510, D:Y.567, D:R.568 Salt bridges: D:R.266, D:R.270, D:R.270, D:K.507, D:R.568, D:K.569, D:K.569

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: E.1882, E.1946, T.2581 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.1946, A:E.1946, A:T.2581 CA.7: 3 residues within 4Å: Chain B: E.1882, E.1946, T.2581 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.1946, B:T.2581 CA.11: 3 residues within 4Å: Chain C: E.1882, E.1946, T.2581 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.1882, C:E.1946, C:T.2581 CA.15: 4 residues within 4Å: Chain D: E.1882, N.1883, E.1946, T.2581 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.1946, D:E.1946, D:T.2581

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

ATP.4: 13 residues within 4Å: Chain A: K.2152, F.2156, T.2537, C.2538, F.2539, I.2540, F.2555, 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, A:W.2566 Salt bridges: A:K.2152, A:K.2560, A:K.2560, A:K.2560 ATP.8: 13 residues within 4Å: Chain B: K.2152, F.2156, T.2537, C.2538, F.2539, I.2540, F.2555, I.2559, K.2560, H.2563, N.2564, M.2565, W.2566 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:F.2539, B:I.2540, B:N.2564, B:M.2565, B:W.2566 Salt bridges: B:K.2152, B:K.2560, B:K.2560, B:K.2560 ATP.12: 12 residues within 4Å: Chain C: K.2152, F.2156, T.2537, C.2538, F.2539, I.2540, I.2559, K.2560, H.2563, N.2564, M.2565, W.2566 9 PLIP interactions: 9 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.2560, C:K.2560, C:K.2560 ATP.16: 12 residues within 4Å: Chain D: K.2152, F.2156, T.2537, 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, D:W.2566 Salt bridges: D:K.2152, D:K.2560, D:K.2560, D:K.2560

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paknejad, N. et al., Structural titration reveals Ca 2+ -dependent conformational landscape of the IP 3 receptor. Nat Commun (2023)

Release Date

2023-11-08

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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