SMTL ID : 8tkg.1

Human Type 3 IP3 Receptor - Resting State (+IP3/ATP)

Coordinates

PDB Format Compare

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.13: 5 residues within 4Å: Chain B: C.2538, I.2540, 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.24: 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.37: 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 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.567, A:Y.567, A:R.568 Salt bridges: A:R.266, A:R.270, A:R.270, A:K.507, A:R.510, A:R.568, A:K.569, A:K.569 I3P.14: 9 residues within 4Å: Chain B: R.266, T.268, L.269, R.270, K.507, R.510, Y.567, R.568, K.569 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.567, B:Y.567, B:R.568 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.25: 9 residues within 4Å: Chain C: R.266, T.268, L.269, R.270, K.507, R.510, Y.567, R.568, K.569 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Y.567, C:Y.567, C:R.568 Salt bridges: C:R.266, C:R.270, C:R.270, C:K.507, C:R.510, C:R.568, C:K.569, C:K.569 I3P.38: 9 residues within 4Å: Chain D: R.266, T.268, L.269, R.270, K.507, R.510, Y.567, R.568, K.569 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:Y.567, D:Y.567, D:R.568 Salt bridges: D:R.266, D:R.270, D:R.270, D:K.507, D:R.510, D:R.568, D:K.569, D:K.569

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: E.1882, N.1883, E.1946, T.2581 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.1882, A:E.1882, A:E.1946, A:T.2581, H2O.2 CA.4: 4 residues within 4Å: Chain A: R.743, Q.744, Y.745, E.1125 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:R.743, A:E.1125, A:E.1125 CA.15: 4 residues within 4Å: Chain B: E.1882, N.1883, E.1946, T.2581 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.1882, B:E.1882, B:E.1946, B:T.2581, H2O.8 CA.16: 4 residues within 4Å: Chain B: R.743, Q.744, Y.745, E.1125 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:R.743, B:E.1125, B:E.1125 CA.26: 4 residues within 4Å: Chain C: E.1882, N.1883, E.1946, T.2581 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.1882, C:E.1882, C:E.1946, C:T.2581, H2O.14 CA.27: 4 residues within 4Å: Chain C: R.743, Q.744, Y.745, E.1125 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:R.743, C:E.1125, C:E.1125 CA.39: 4 residues within 4Å: Chain D: E.1882, N.1883, E.1946, T.2581 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.1882, D:E.1882, D:E.1946, D:T.2581, H2O.20 CA.40: 4 residues within 4Å: Chain D: R.743, Q.744, Y.745, E.1125 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:R.743, D:E.1125, D:E.1125

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

ATP.5: 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 Salt bridges: A:K.2152, A:K.2152, A:K.2560, A:K.2560, A:K.2560 ATP.17: 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 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.28: 13 residues within 4Å: Chain C: 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 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.41: 13 residues within 4Å: Chain D: 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 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

24 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Covalent)

PCW.6: 19 residues within 4Å: Chain A: R.2304, M.2318, E.2319, L.2321, Y.2322, G.2325, Y.2326, T.2329, I.2343, L.2344, F.2346, D.2347, I.2349, Y.2350, R.2351, E.2353, F.2356 Ligands: PCW.7, PCW.8 Ligand excluded by PLIP PCW.7: 16 residues within 4Å: Chain A: M.2318, F.2346, I.2349, F.2356, I.2359, K.2360, V.2362, T.2363 Chain D: L.2375, L.2379, I.2503, I.2507, V.2508 Ligands: PCW.6, PCW.8, PCW.34 Ligand excluded by PLIP PCW.8: 14 residues within 4Å: Chain A: Y.2223, H.2337, L.2339, F.2340, S.2342, I.2343, F.2346 Chain D: L.2382, I.2385, V.2386, L.2389, F.2390 Ligands: PCW.6, PCW.7 Ligand excluded by PLIP PCW.9: 15 residues within 4Å: Chain A: F.2502, I.2503, I.2506, I.2507 Chain B: V.2362, T.2363, R.2364, G.2366, R.2367, I.2369, L.2370, A.2373, I.2512 Ligands: PCW.10, PCW.19 Ligand excluded by PLIP PCW.10: 14 residues within 4Å: Chain A: K.2485, F.2490, P.2491, V.2494, V.2495, L.2498, L.2499, F.2502 Chain B: L.2459, M.2460, V.2463, M.2466 Ligands: PCW.9, PCW.23 Ligand excluded by PLIP PCW.11: 24 residues within 4Å: Chain A: F.2209, N.2210, V.2213, F.2214, N.2216, I.2217, A.2220, F.2221, R.2262, L.2345, L.2348, R.2351, E.2352 Chain C: L.2498 Chain D: R.2367, L.2371, L.2374, L.2377, I.2378, Y.2381, L.2459, I.2462, M.2466 Ligands: PCW.33 Ligand excluded by PLIP PCW.12: 24 residues within 4Å: Chain A: R.2367, L.2371, L.2374, L.2377, I.2378, Y.2381, L.2459, I.2462, M.2466 Chain B: F.2209, N.2210, V.2213, F.2214, N.2216, I.2217, A.2220, F.2221, R.2262, L.2345, L.2348, R.2351, E.2352 Chain D: L.2498 Ligands: PCW.35 Ligand excluded by PLIP PCW.18: 19 residues within 4Å: Chain B: R.2304, M.2318, E.2319, L.2321, Y.2322, G.2325, Y.2326, T.2329, I.2343, L.2344, F.2346, D.2347, I.2349, Y.2350, R.2351, E.2353, F.2356 Ligands: PCW.19, PCW.20 Ligand excluded by PLIP PCW.19: 16 residues within 4Å: Chain A: L.2375, L.2379, I.2503, I.2507, V.2508 Chain B: M.2318, F.2346, I.2349, F.2356, I.2359, K.2360, V.2362, T.2363 Ligands: PCW.9, PCW.18, PCW.20 Ligand excluded by PLIP PCW.20: 15 residues within 4Å: Chain A: L.2382, I.2385, V.2386, F.2388, L.2389, F.2390 Chain B: Y.2223, H.2337, L.2339, F.2340, S.2342, I.2343, F.2346 Ligands: PCW.18, PCW.19 Ligand excluded by PLIP PCW.21: 15 residues within 4Å: Chain B: F.2502, I.2503, I.2506, I.2507 Chain C: V.2362, T.2363, R.2364, G.2366, R.2367, I.2369, L.2370, A.2373, I.2512 Ligands: PCW.22, PCW.30 Ligand excluded by PLIP PCW.22: 14 residues within 4Å: Chain B: K.2485, F.2490, P.2491, V.2494, V.2495, L.2498, L.2499, F.2502 Chain C: L.2459, M.2460, V.2463, M.2466 Ligands: PCW.21, PCW.36 Ligand excluded by PLIP PCW.23: 24 residues within 4Å: Chain A: L.2498 Chain B: R.2367, L.2371, L.2374, L.2377, I.2378, Y.2381, L.2459, I.2462, M.2466 Chain C: F.2209, N.2210, V.2213, F.2214, N.2216, I.2217, A.2220, F.2221, R.2262, L.2345, L.2348, R.2351, E.2352 Ligands: PCW.10 Ligand excluded by PLIP PCW.29: 19 residues within 4Å: Chain C: R.2304, M.2318, E.2319, L.2321, Y.2322, G.2325, Y.2326, T.2329, I.2343, L.2344, F.2346, D.2347, I.2349, Y.2350, R.2351, E.2353, F.2356 Ligands: PCW.30, PCW.31 Ligand excluded by PLIP PCW.30: 16 residues within 4Å: Chain B: L.2375, L.2379, I.2503, I.2507, V.2508 Chain C: M.2318, F.2346, I.2349, F.2356, I.2359, K.2360, V.2362, T.2363 Ligands: PCW.21, PCW.29, PCW.31 Ligand excluded by PLIP PCW.31: 15 residues within 4Å: Chain B: L.2382, I.2385, V.2386, F.2388, L.2389, F.2390 Chain C: Y.2223, H.2337, L.2339, F.2340, S.2342, I.2343, F.2346 Ligands: PCW.29, PCW.30 Ligand excluded by PLIP PCW.32: 15 residues within 4Å: Chain C: F.2502, I.2503, I.2506, I.2507 Chain D: V.2362, T.2363, R.2364, G.2366, R.2367, I.2369, L.2370, A.2373, I.2512 Ligands: PCW.33, PCW.43 Ligand excluded by PLIP PCW.33: 14 residues within 4Å: Chain C: K.2485, F.2490, P.2491, V.2494, V.2495, L.2498, L.2499, F.2502 Chain D: L.2459, M.2460, V.2463, M.2466 Ligands: PCW.11, PCW.32 Ligand excluded by PLIP PCW.34: 15 residues within 4Å: Chain A: V.2362, T.2363, R.2364, G.2366, R.2367, I.2369, L.2370, A.2373, I.2512 Chain D: F.2502, I.2503, I.2506, I.2507 Ligands: PCW.7, PCW.35 Ligand excluded by PLIP PCW.35: 14 residues within 4Å: Chain A: L.2459, M.2460, V.2463, M.2466 Chain D: K.2485, F.2490, P.2491, V.2494, V.2495, L.2498, L.2499, F.2502 Ligands: PCW.12, PCW.34 Ligand excluded by PLIP PCW.36: 24 residues within 4Å: Chain B: L.2498 Chain C: R.2367, L.2371, L.2374, L.2377, I.2378, Y.2381, L.2459, I.2462, M.2466 Chain D: F.2209, N.2210, V.2213, F.2214, N.2216, I.2217, A.2220, F.2221, R.2262, L.2345, L.2348, R.2351, E.2352 Ligands: PCW.22 Ligand excluded by PLIP PCW.42: 19 residues within 4Å: Chain D: R.2304, M.2318, E.2319, L.2321, Y.2322, G.2325, Y.2326, T.2329, I.2343, L.2344, F.2346, D.2347, I.2349, Y.2350, R.2351, E.2353, F.2356 Ligands: PCW.43, PCW.44 Ligand excluded by PLIP PCW.43: 15 residues within 4Å: Chain C: L.2375, L.2379, I.2507, V.2508 Chain D: M.2318, F.2346, I.2349, F.2356, I.2359, K.2360, V.2362, T.2363 Ligands: PCW.32, PCW.42, PCW.44 Ligand excluded by PLIP PCW.44: 15 residues within 4Å: Chain C: L.2382, I.2385, V.2386, F.2388, L.2389, F.2390 Chain D: Y.2223, H.2337, L.2339, F.2340, S.2342, I.2343, F.2346 Ligands: PCW.42, PCW.43 Ligand excluded by PLIP

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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