SMTL ID : 8ear.1

Structure of the full-length IP3R1 channel determined in the presence of Calcium/IP3/ATP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.2611, C.2614, H.2631, H.2636 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.2611, A:C.2614, A:H.2631 ZN.15: 4 residues within 4Å: Chain B: C.2611, C.2614, H.2631, H.2636 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.2611, B:C.2614, B:H.2631 ZN.29: 4 residues within 4Å: Chain C: C.2611, C.2614, H.2631, H.2636 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.2611, C:C.2614, C:H.2631 ZN.43: 4 residues within 4Å: Chain D: C.2611, C.2614, H.2631, H.2636 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.2611, D:C.2614, D:H.2631

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

ATP.2: 12 residues within 4Å: Chain A: K.2221, K.2224, Y.2228, C.2611, F.2612, I.2613, I.2632, K.2633, H.2636, N.2637, M.2638, W.2639 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.2228, A:F.2612, A:I.2613, A:K.2633, A:H.2636, A:M.2638 Salt bridges: A:K.2221, A:K.2221, A:K.2224, A:K.2224, A:K.2633 ATP.17: 12 residues within 4Å: Chain B: K.2221, K.2224, Y.2228, C.2611, F.2612, I.2613, I.2632, K.2633, H.2636, N.2637, M.2638, W.2639 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.2228, B:F.2612, B:I.2613, B:K.2633, B:H.2636, B:M.2638 Salt bridges: B:K.2221, B:K.2221, B:K.2224, B:K.2224, B:K.2633 ATP.35: 12 residues within 4Å: Chain C: K.2221, K.2224, Y.2228, C.2611, F.2612, I.2613, I.2632, K.2633, H.2636, N.2637, M.2638, W.2639 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Y.2228, C:F.2612, C:I.2613, C:K.2633, C:H.2636, C:M.2638 Salt bridges: C:K.2221, C:K.2221, C:K.2224, C:K.2224, C:K.2633 ATP.45: 12 residues within 4Å: Chain D: K.2221, K.2224, Y.2228, C.2611, F.2612, I.2613, I.2632, K.2633, H.2636, N.2637, M.2638, W.2639 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:Y.2228, D:F.2612, D:I.2613, D:K.2633, D:H.2636, D:M.2638 Salt bridges: D:K.2221, D:K.2221, D:K.2224, D:K.2224, D:K.2633

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

I3P.3: 5 residues within 4Å: Chain A: R.265, G.268, R.269, Y.567, K.569 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.268, A:G.268, A:R.269, A:R.269, A:Y.567 Salt bridges: A:R.265 I3P.18: 5 residues within 4Å: Chain B: R.265, G.268, R.269, Y.567, K.569 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.268, B:G.268, B:R.269, B:R.269, B:Y.567 Salt bridges: B:R.265 I3P.36: 5 residues within 4Å: Chain C: R.265, G.268, R.269, Y.567, K.569 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.268, C:G.268, C:R.269, C:R.269, C:Y.567 Salt bridges: C:R.265 I3P.46: 5 residues within 4Å: Chain D: R.265, G.268, R.269, Y.567, K.569 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.268, D:G.268, D:R.269, D:R.269, D:Y.567 Salt bridges: D:R.265

16 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: N.2583 Chain B: F.2586 No protein-ligand interaction detected (PLIP) CA.5: 2 residues within 4Å: Chain A: F.53, E.283 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: Q.2045, Y.2656 No protein-ligand interaction detected (PLIP) CA.7: 4 residues within 4Å: Chain A: H.2541, R.2544, S.2545 Chain D: D.2551 No protein-ligand interaction detected (PLIP) CA.19: 2 residues within 4Å: Chain B: N.2583 Chain C: F.2586 No protein-ligand interaction detected (PLIP) CA.20: 2 residues within 4Å: Chain B: F.53, E.283 No protein-ligand interaction detected (PLIP) CA.21: 2 residues within 4Å: Chain B: Q.2045, Y.2656 No protein-ligand interaction detected (PLIP) CA.22: 4 residues within 4Å: Chain A: D.2551 Chain B: H.2541, R.2544, S.2545 No protein-ligand interaction detected (PLIP) CA.37: 2 residues within 4Å: Chain C: N.2583 Chain D: F.2586 No protein-ligand interaction detected (PLIP) CA.38: 2 residues within 4Å: Chain C: F.53, E.283 No protein-ligand interaction detected (PLIP) CA.39: 2 residues within 4Å: Chain C: Q.2045, Y.2656 No protein-ligand interaction detected (PLIP) CA.40: 4 residues within 4Å: Chain B: D.2551 Chain C: H.2541, R.2544, S.2545 No protein-ligand interaction detected (PLIP) CA.47: 2 residues within 4Å: Chain A: F.2586 Chain D: N.2583 No protein-ligand interaction detected (PLIP) CA.48: 2 residues within 4Å: Chain D: F.53, E.283 No protein-ligand interaction detected (PLIP) CA.49: 2 residues within 4Å: Chain D: Q.2045, Y.2656 No protein-ligand interaction detected (PLIP) CA.50: 4 residues within 4Å: Chain C: D.2551 Chain D: H.2541, R.2544, S.2545 No protein-ligand interaction detected (PLIP)

28 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)(Covalent)

PLX.8: 8 residues within 4Å: Chain A: L.2289, R.2334, L.2417, L.2420, R.2423 Chain D: L.2443, L.2449, Y.2453 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.2289, A:L.2417, D:L.2449, D:Y.2453 PLX.9: 9 residues within 4Å: Chain A: T.2530, L.2532, M.2533, V.2536 Chain B: L.2305 Chain D: F.2563, A.2564, I.2568, L.2571 7 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 4 interactions with chain D Salt bridges: B:H.2308 Hydrophobic interactions: A:L.2532, A:V.2536, D:A.2564, D:I.2568, D:I.2568, D:L.2571 PLX.10: 9 residues within 4Å: Chain A: H.2409, F.2411, F.2412, S.2414, L.2415 Chain D: I.2457, L.2461, F.2462 Ligands: PLX.56 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:H.2409, A:F.2411, A:L.2415, D:I.2457, D:F.2462, D:F.2462 Hydrogen bonds: A:V.2408 Salt bridges: A:H.2409, A:H.2409 PLX.11: 3 residues within 4Å: Chain A: T.2435, R.2439 Ligands: PLX.13 No protein-ligand interaction detected (PLIP) PLX.12: 9 residues within 4Å: Chain A: L.2393, Y.2394, Y.2398, F.2418, V.2421, Y.2422, E.2425, L.2428 Ligands: PLX.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.2393, A:Y.2394, A:Y.2394, A:F.2418, A:F.2418, A:V.2421, A:Y.2422 Salt bridges: A:E.2425 PLX.13: 10 residues within 4Å: Chain A: L.2428, I.2431, K.2432, V.2434, T.2435, R.2436 Chain D: M.2576, I.2580 Ligands: PLX.11, PLX.12 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.2434, A:T.2435, D:I.2580 Salt bridges: A:K.2432, A:K.2432 PLX.14: 4 residues within 4Å: Chain A: V.2458, F.2462, L.2562 Ligands: PLX.25 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.2458, A:F.2462, A:L.2562 PLX.16: 4 residues within 4Å: Chain B: V.2458, F.2462, L.2562 Ligands: PLX.31 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.2458, B:F.2462, B:L.2562 PLX.23: 8 residues within 4Å: Chain A: L.2443, L.2449, Y.2453 Chain B: L.2289, R.2334, L.2417, L.2420, R.2423 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.2289, B:L.2417, A:L.2449, A:Y.2453 PLX.24: 9 residues within 4Å: Chain A: F.2563, A.2564, I.2568, L.2571 Chain B: T.2530, L.2532, M.2533, V.2536 Chain C: L.2305 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:A.2564, A:I.2568, A:I.2568, A:L.2571, B:L.2532, B:V.2536 Salt bridges: C:H.2308 PLX.25: 9 residues within 4Å: Chain A: I.2457, L.2461, F.2462 Chain B: H.2409, F.2411, F.2412, S.2414, L.2415 Ligands: PLX.14 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.2457, A:F.2462, A:F.2462, B:H.2409, B:F.2411, B:L.2415 Hydrogen bonds: B:V.2408 Salt bridges: B:H.2409, B:H.2409 PLX.26: 2 residues within 4Å: Chain B: T.2435 Ligands: PLX.28 No protein-ligand interaction detected (PLIP) PLX.27: 9 residues within 4Å: Chain B: L.2393, Y.2394, Y.2398, F.2418, V.2421, Y.2422, E.2425, L.2428 Ligands: PLX.28 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.2393, B:Y.2394, B:Y.2394, B:F.2418, B:F.2418, B:V.2421, B:Y.2422 Salt bridges: B:E.2425 PLX.28: 10 residues within 4Å: Chain A: M.2576, I.2580 Chain B: L.2428, I.2431, K.2432, V.2434, T.2435, R.2436 Ligands: PLX.26, PLX.27 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.2580, B:V.2434, B:T.2435 Salt bridges: B:K.2432, B:K.2432 PLX.30: 9 residues within 4Å: Chain B: F.2563, A.2564, I.2568, L.2571 Chain C: T.2530, L.2532, M.2533, V.2536 Chain D: L.2305 7 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: C:L.2532, C:V.2536, B:A.2564, B:I.2568, B:I.2568, B:L.2571 Salt bridges: D:H.2308 PLX.31: 9 residues within 4Å: Chain B: I.2457, L.2461, F.2462 Chain C: H.2409, F.2411, F.2412, S.2414, L.2415 Ligands: PLX.16 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:H.2409, C:F.2411, C:L.2415, B:I.2457, B:F.2462, B:F.2462 Hydrogen bonds: C:V.2408 Salt bridges: C:H.2409, C:H.2409 PLX.32: 3 residues within 4Å: Chain C: T.2435, R.2439 Ligands: PLX.34 No protein-ligand interaction detected (PLIP) PLX.33: 9 residues within 4Å: Chain C: L.2393, Y.2394, Y.2398, F.2418, V.2421, Y.2422, E.2425, L.2428 Ligands: PLX.34 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.2393, C:Y.2394, C:Y.2394, C:F.2418, C:F.2418, C:V.2421, C:Y.2422 Salt bridges: C:E.2425 PLX.34: 10 residues within 4Å: Chain B: M.2576, I.2580 Chain C: L.2428, I.2431, K.2432, V.2434, T.2435, R.2436 Ligands: PLX.32, PLX.33 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.2434, C:T.2435, B:I.2580 Salt bridges: C:K.2432, C:K.2432 PLX.41: 4 residues within 4Å: Chain C: V.2458, F.2462, L.2562 Ligands: PLX.52 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.2458, C:F.2462, C:L.2562 PLX.42: 8 residues within 4Å: Chain B: L.2443, L.2449, Y.2453 Chain C: L.2289, R.2334, L.2417, L.2420, R.2423 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.2449, B:Y.2453, C:L.2289, C:L.2417 PLX.44: 8 residues within 4Å: Chain C: L.2443, L.2449, Y.2453 Chain D: L.2289, R.2334, L.2417, L.2420, R.2423 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.2449, C:Y.2453, D:L.2289, D:L.2417 PLX.51: 9 residues within 4Å: Chain A: L.2305 Chain C: F.2563, A.2564, I.2568, L.2571 Chain D: T.2530, L.2532, M.2533, V.2536 7 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: C:A.2564, C:I.2568, C:I.2568, C:L.2571, D:L.2532, D:V.2536 Salt bridges: A:H.2308 PLX.52: 9 residues within 4Å: Chain C: I.2457, L.2461, F.2462 Chain D: H.2409, F.2411, F.2412, S.2414, L.2415 Ligands: PLX.41 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:I.2457, C:F.2462, C:F.2462, D:H.2409, D:F.2411, D:L.2415 Hydrogen bonds: D:V.2408 Salt bridges: D:H.2409, D:H.2409 PLX.53: 2 residues within 4Å: Chain D: T.2435 Ligands: PLX.55 No protein-ligand interaction detected (PLIP) PLX.54: 9 residues within 4Å: Chain D: L.2393, Y.2394, Y.2398, F.2418, V.2421, Y.2422, E.2425, L.2428 Ligands: PLX.55 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.2393, D:Y.2394, D:Y.2394, D:F.2418, D:F.2418, D:V.2421, D:Y.2422 Salt bridges: D:E.2425 PLX.55: 10 residues within 4Å: Chain C: M.2576, I.2580 Chain D: L.2428, I.2431, K.2432, V.2434, T.2435, R.2436 Ligands: PLX.53, PLX.54 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.2434, D:T.2435, C:I.2580 Salt bridges: D:K.2432, D:K.2432 PLX.56: 4 residues within 4Å: Chain D: V.2458, F.2462, L.2562 Ligands: PLX.10 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.2458, D:F.2462, D:L.2562

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, G. et al., Conformational motions and ligand-binding underlying gating and regulation in IP 3 R channel. Nat Commun (2022)

Release Date

2022-11-23

Peptides

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

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