SMTL ID : 8tkf.1

Human Type 3 IP3 Receptor - Activated State (+IP3/ATP/JD Ca2+)

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.11: 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.20: 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.29: 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: 11 residues within 4Å: Chain A: R.266, T.268, L.269, R.270, A.276, R.503, K.507, R.510, Y.567, R.568, K.569 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.268, A:L.269, A:Y.567, A:Y.567 Salt bridges: A:R.266, A:R.270, A:K.507, A:R.510, A:R.568, A:K.569, A:K.569 I3P.12: 11 residues within 4Å: Chain B: R.266, T.268, L.269, R.270, A.276, R.503, K.507, R.510, Y.567, R.568, K.569 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.268, B:L.269, B:Y.567, B:Y.567 Salt bridges: B:R.266, B:R.270, B:K.507, B:R.510, B:R.568, B:K.569, B:K.569 I3P.21: 11 residues within 4Å: Chain C: R.266, T.268, L.269, R.270, A.276, R.503, K.507, R.510, Y.567, R.568, K.569 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.268, C:L.269, C:Y.567, C:Y.567 Salt bridges: C:R.266, C:R.270, C:K.507, C:R.510, C:R.568, C:K.569, C:K.569 I3P.30: 11 residues within 4Å: Chain D: R.266, T.268, L.269, R.270, A.276, R.503, K.507, R.510, Y.567, R.568, K.569 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:T.268, D:L.269, D:Y.567, D:Y.567 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 CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: E.1882, E.1946, T.2581 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.1882, A:E.1882, A:E.1946, A:E.1946 CA.13: 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.1882, B:E.1946, B:E.1946 CA.22: 3 residues within 4Å: Chain C: E.1882, E.1946, T.2581 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.1882, C:E.1882, C:E.1946, C:E.1946 CA.31: 3 residues within 4Å: Chain D: E.1882, E.1946, T.2581 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.1882, D:E.1882, D:E.1946, D:E.1946

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

ATP.4: 13 residues within 4Å: Chain A: E.2149, 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 A Hydrogen bonds: A:F.2539, 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.14: 13 residues within 4Å: Chain B: E.2149, 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 B Hydrogen bonds: B:F.2539, B:H.2563, B:N.2564, B:M.2565, B:W.2566 Salt bridges: B:K.2152, B:K.2560, B:K.2560, B:K.2560 ATP.23: 13 residues within 4Å: Chain C: E.2149, 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:H.2563, C:N.2564, C:M.2565, C:W.2566 Salt bridges: C:K.2152, C:K.2560, C:K.2560, C:K.2560 ATP.32: 13 residues within 4Å: Chain D: E.2149, 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 D Hydrogen bonds: D:F.2539, 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

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

PCW.5: 18 residues within 4Å: Chain A: M.2318, E.2319, L.2321, Y.2322, G.2325, Y.2326, T.2329, F.2346, I.2349, Y.2350, F.2356, I.2359 Chain D: L.2379, L.2382, F.2383, I.2503 Ligands: PCW.6, PCW.8 Ligand excluded by PLIP PCW.6: 20 residues within 4Å: Chain A: I.2349, Y.2350, F.2356, V.2358, I.2359, K.2360, V.2362, T.2363, G.2366, I.2369, L.2370, F.2513, I.2516 Chain D: L.2375, L.2379, F.2502, I.2503, I.2507, V.2508 Ligands: PCW.5 Ligand excluded by PLIP PCW.7: 22 residues within 4Å: Chain A: T.2457, L.2459, M.2460, V.2463, M.2466 Chain B: F.2221, S.2230, G.2232, V.2233, S.2236, L.2238, L.2242 Chain D: K.2485, D.2486, F.2490, P.2491, V.2494, V.2495, L.2498, L.2499, F.2502 Ligands: PT5.10 Ligand excluded by PLIP PCW.8: 16 residues within 4Å: Chain A: Y.2223, Y.2322, Y.2326, H.2337, L.2339, F.2340, S.2342, I.2343, F.2346 Chain D: L.2382, I.2385, V.2386, F.2388, L.2389, F.2390 Ligands: PCW.5 Ligand excluded by PLIP PCW.15: 18 residues within 4Å: Chain A: L.2379, L.2382, F.2383, I.2503 Chain B: M.2318, E.2319, L.2321, Y.2322, G.2325, Y.2326, T.2329, F.2346, I.2349, Y.2350, F.2356, I.2359 Ligands: PCW.16, PCW.18 Ligand excluded by PLIP PCW.16: 19 residues within 4Å: Chain A: L.2375, L.2379, F.2502, I.2503, I.2507 Chain B: I.2349, Y.2350, F.2356, V.2358, I.2359, K.2360, V.2362, T.2363, G.2366, I.2369, L.2370, F.2513, I.2516 Ligands: PCW.15 Ligand excluded by PLIP PCW.17: 22 residues within 4Å: Chain A: K.2485, D.2486, F.2490, P.2491, V.2494, V.2495, L.2498, L.2499, F.2502 Chain B: T.2457, L.2459, M.2460, V.2463, M.2466 Chain C: F.2221, S.2230, G.2232, V.2233, S.2236, L.2238, L.2242 Ligands: PT5.19 Ligand excluded by PLIP PCW.18: 16 residues within 4Å: Chain A: L.2382, I.2385, V.2386, F.2388, L.2389, F.2390 Chain B: Y.2223, Y.2322, Y.2326, H.2337, L.2339, F.2340, S.2342, I.2343, F.2346 Ligands: PCW.15 Ligand excluded by PLIP PCW.24: 18 residues within 4Å: Chain B: L.2379, L.2382, F.2383, I.2503 Chain C: M.2318, E.2319, L.2321, Y.2322, G.2325, Y.2326, T.2329, F.2346, I.2349, Y.2350, F.2356, I.2359 Ligands: PCW.25, PCW.27 Ligand excluded by PLIP PCW.25: 20 residues within 4Å: Chain B: L.2375, L.2379, F.2502, I.2503, I.2507, V.2508 Chain C: I.2349, Y.2350, F.2356, V.2358, I.2359, K.2360, V.2362, T.2363, G.2366, I.2369, L.2370, F.2513, I.2516 Ligands: PCW.24 Ligand excluded by PLIP PCW.26: 22 residues within 4Å: Chain B: K.2485, D.2486, F.2490, P.2491, V.2494, V.2495, L.2498, L.2499, F.2502 Chain C: T.2457, L.2459, M.2460, V.2463, M.2466 Chain D: F.2221, S.2230, G.2232, V.2233, S.2236, L.2238, L.2242 Ligands: PT5.28 Ligand excluded by PLIP PCW.27: 16 residues within 4Å: Chain B: L.2382, I.2385, V.2386, F.2388, L.2389, F.2390 Chain C: Y.2223, Y.2322, Y.2326, H.2337, L.2339, F.2340, S.2342, I.2343, F.2346 Ligands: PCW.24 Ligand excluded by PLIP PCW.33: 18 residues within 4Å: Chain C: L.2379, L.2382, F.2383, I.2503 Chain D: M.2318, E.2319, L.2321, Y.2322, G.2325, Y.2326, T.2329, F.2346, I.2349, Y.2350, F.2356, I.2359 Ligands: PCW.34, PCW.36 Ligand excluded by PLIP PCW.34: 20 residues within 4Å: Chain C: L.2375, L.2379, F.2502, I.2503, I.2507, V.2508 Chain D: I.2349, Y.2350, F.2356, V.2358, I.2359, K.2360, V.2362, T.2363, G.2366, I.2369, L.2370, F.2513, I.2516 Ligands: PCW.33 Ligand excluded by PLIP PCW.35: 22 residues within 4Å: Chain A: F.2221, S.2230, G.2232, V.2233, S.2236, L.2238, L.2242 Chain C: K.2485, D.2486, F.2490, P.2491, V.2494, V.2495, L.2498, L.2499, F.2502 Chain D: T.2457, L.2459, M.2460, V.2463, M.2466 Ligands: PT5.9 Ligand excluded by PLIP PCW.36: 16 residues within 4Å: Chain C: L.2382, I.2385, V.2386, F.2388, L.2389, F.2390 Chain D: Y.2223, Y.2322, Y.2326, H.2337, L.2339, F.2340, S.2342, I.2343, F.2346 Ligands: PCW.33 Ligand excluded by PLIP

4 x PT5: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)

PT5.9: 32 residues within 4Å: Chain A: T.2202, G.2205, S.2206, F.2209, N.2210, V.2213, F.2214, N.2216, I.2217, A.2220, F.2221, L.2242, L.2246, Y.2259, R.2262, V.2266, L.2345, L.2348, R.2351, E.2352, L.2355 Chain D: R.2367, L.2371, L.2374, L.2377, I.2378, Y.2381, L.2459, I.2462, V.2463, M.2466 Ligands: PCW.35 18 PLIP interactions: 11 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:N.2216, A:A.2220, A:L.2242, A:R.2262, D:L.2374, D:L.2374, D:L.2377, D:I.2378, D:I.2378, D:L.2459 Hydrogen bonds: A:S.2206, A:N.2210, A:R.2262, A:E.2352, A:E.2352 Salt bridges: A:R.2262, A:R.2262, D:R.2367 PT5.10: 32 residues within 4Å: Chain A: R.2367, L.2371, L.2374, L.2377, I.2378, Y.2381, L.2459, I.2462, V.2463, M.2466 Chain B: T.2202, G.2205, S.2206, F.2209, N.2210, V.2213, F.2214, N.2216, I.2217, A.2220, F.2221, L.2242, L.2246, Y.2259, R.2262, V.2266, L.2345, L.2348, R.2351, E.2352, L.2355 Ligands: PCW.7 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:A.2220, B:L.2242, B:R.2262, A:L.2374, A:L.2374, A:L.2377, A:I.2378, A:I.2378, A:L.2459 Hydrogen bonds: B:S.2206, B:N.2210, B:R.2262, B:E.2352 Salt bridges: B:R.2262, B:R.2262, A:R.2367 PT5.19: 32 residues within 4Å: Chain B: R.2367, L.2371, L.2374, L.2377, I.2378, Y.2381, L.2459, I.2462, V.2463, M.2466 Chain C: T.2202, G.2205, S.2206, F.2209, N.2210, V.2213, F.2214, N.2216, I.2217, A.2220, F.2221, L.2242, L.2246, Y.2259, R.2262, V.2266, L.2345, L.2348, R.2351, E.2352, L.2355 Ligands: PCW.17 19 PLIP interactions: 7 interactions with chain B, 12 interactions with chain C Hydrophobic interactions: B:L.2374, B:L.2374, B:L.2377, B:I.2378, B:I.2378, B:L.2459, C:N.2216, C:I.2217, C:A.2220, C:L.2242, C:R.2262 Salt bridges: B:R.2367, C:R.2262, C:R.2262 Hydrogen bonds: C:S.2206, C:N.2210, C:R.2262, C:E.2352, C:E.2352 PT5.28: 32 residues within 4Å: Chain C: R.2367, L.2371, L.2374, L.2377, I.2378, Y.2381, L.2459, I.2462, V.2463, M.2466 Chain D: T.2202, G.2205, S.2206, F.2209, N.2210, V.2213, F.2214, N.2216, I.2217, A.2220, F.2221, L.2242, L.2246, Y.2259, R.2262, V.2266, L.2345, L.2348, R.2351, E.2352, L.2355 Ligands: PCW.26 18 PLIP interactions: 11 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:N.2216, D:A.2220, D:L.2242, D:R.2262, C:L.2374, C:L.2374, C:L.2377, C:I.2378, C:I.2378, C:L.2459 Hydrogen bonds: D:S.2206, D:N.2210, D:R.2262, D:E.2352, D:E.2352 Salt bridges: D:R.2262, D:R.2262, C:R.2367

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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