SMTL ID : 8eaq.1

Structure of the full-length IP3R1 channel determined at high Ca2+

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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.2611, A:C.2614, A:H.2631, A:H.2636 ZN.15: 4 residues within 4Å: Chain B: C.2611, C.2614, H.2631, H.2636 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.2611, B:C.2614, B:H.2631, B:H.2636 ZN.28: 4 residues within 4Å: Chain C: C.2611, C.2614, H.2631, H.2636 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.2611, C:C.2614, C:H.2631, C:H.2636 ZN.41: 4 residues within 4Å: Chain D: C.2611, C.2614, H.2631, H.2636 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.2611, D:C.2614, D:H.2631, D:H.2636

20 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: D.2551 Chain C: S.2545 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: S.2545 Chain B: D.2551 No protein-ligand interaction detected (PLIP) CA.4: 2 residues within 4Å: Chain A: N.2583 Chain C: L.2582 No protein-ligand interaction detected (PLIP) CA.5: 2 residues within 4Å: Chain A: K.52, K.306 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: E.2042, T.2654 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: D.180 Chain C: D.426 No protein-ligand interaction detected (PLIP) CA.16: 2 residues within 4Å: Chain B: S.2545 Chain D: D.2551 No protein-ligand interaction detected (PLIP) CA.17: 2 residues within 4Å: Chain A: L.2582 Chain B: N.2583 No protein-ligand interaction detected (PLIP) CA.18: 2 residues within 4Å: Chain B: K.52, K.306 No protein-ligand interaction detected (PLIP) CA.19: 2 residues within 4Å: Chain B: E.2042, T.2654 No protein-ligand interaction detected (PLIP) CA.20: 2 residues within 4Å: Chain A: D.426 Chain B: D.180 No protein-ligand interaction detected (PLIP) CA.29: 2 residues within 4Å: Chain C: D.2551 Chain D: S.2545 No protein-ligand interaction detected (PLIP) CA.30: 2 residues within 4Å: Chain C: N.2583 Chain D: L.2582 No protein-ligand interaction detected (PLIP) CA.31: 2 residues within 4Å: Chain C: K.52, K.306 No protein-ligand interaction detected (PLIP) CA.32: 2 residues within 4Å: Chain C: E.2042, T.2654 No protein-ligand interaction detected (PLIP) CA.33: 2 residues within 4Å: Chain C: D.180 Chain D: D.426 No protein-ligand interaction detected (PLIP) CA.42: 2 residues within 4Å: Chain B: L.2582 Chain D: N.2583 No protein-ligand interaction detected (PLIP) CA.43: 2 residues within 4Å: Chain D: K.52, K.306 No protein-ligand interaction detected (PLIP) CA.44: 2 residues within 4Å: Chain D: E.2042, T.2654 No protein-ligand interaction detected (PLIP) CA.45: 2 residues within 4Å: Chain B: D.426 Chain D: D.180 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(Covalent)(Non-covalent)

PLX.8: 11 residues within 4Å: Chain A: F.2455, V.2458, F.2462, F.2463, P.2561, L.2562, A.2565, I.2568, Y.2569, L.2572 Ligands: PLX.35 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.2455, A:V.2458, A:V.2458, A:F.2462, A:F.2462, A:F.2463, A:L.2562, A:A.2565, A:I.2568, A:Y.2569 PLX.9: 7 residues within 4Å: Chain A: L.2532, M.2533 Chain B: F.2563, A.2564, I.2568, L.2571 Ligands: PLX.27 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.2564, B:I.2568, B:I.2568, B:L.2571 PLX.10: 5 residues within 4Å: Chain A: R.2439 Chain C: F.2281, N.2282, V.2285, L.2420 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.2281, C:V.2285 Salt bridges: A:R.2439 PLX.11: 9 residues within 4Å: Chain A: H.2409, F.2411, F.2412, S.2414, L.2415 Chain B: L.2454, V.2458, L.2461, F.2462 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.2454, B:V.2458, B:L.2461, B:F.2462, A:F.2411, A:L.2415 PLX.12: 6 residues within 4Å: Chain A: T.2435, G.2438, R.2439, I.2441, I.2442 Ligands: PLX.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.2441, A:I.2442 Hydrogen bonds: A:G.2438 PLX.13: 10 residues within 4Å: Chain A: V.2390, E.2391, L.2393, Y.2394, L.2397, F.2418, Y.2422, E.2425, L.2428 Ligands: PLX.14 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.2390, A:E.2391, A:L.2393, A:Y.2394, A:L.2397, A:F.2418, A:F.2418, A:L.2428 Salt bridges: A:E.2425 pi-Cation interactions: A:Y.2422 PLX.14: 9 residues within 4Å: Chain A: V.2421, L.2428, I.2431, K.2432, V.2434, T.2435, R.2436 Ligands: PLX.12, PLX.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.2421, A:L.2428, A:I.2431, A:V.2434, A:T.2435 Salt bridges: A:K.2432 PLX.21: 8 residues within 4Å: Chain B: L.2532, M.2533, V.2536 Chain D: F.2563, A.2564, I.2568, L.2571 Ligands: PLX.52 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:A.2564, D:I.2568, D:I.2568, D:L.2571, B:V.2536 PLX.22: 6 residues within 4Å: Chain A: F.2281, N.2282, V.2285, L.2420 Chain B: R.2439, I.2450 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.2450, A:F.2281, A:V.2285 Salt bridges: B:R.2439 PLX.23: 9 residues within 4Å: Chain B: H.2409, F.2411, F.2412, S.2414, L.2415 Chain D: L.2454, V.2458, L.2461, F.2462 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.2454, D:V.2458, D:L.2461, D:F.2462, B:F.2411, B:L.2415 PLX.24: 8 residues within 4Å: Chain B: V.2434, T.2435, R.2436, G.2438, R.2439, I.2441, I.2442 Ligands: PLX.26 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.2434, B:I.2441, B:I.2442 Hydrogen bonds: B:G.2438 PLX.25: 10 residues within 4Å: Chain B: V.2390, E.2391, L.2393, Y.2394, L.2397, F.2418, Y.2422, E.2425, L.2428 Ligands: PLX.26 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.2390, B:E.2391, B:L.2393, B:Y.2394, B:L.2397, B:L.2397, B:F.2418, B:F.2418, B:L.2428 Salt bridges: B:E.2425 pi-Cation interactions: B:Y.2422 PLX.26: 9 residues within 4Å: Chain B: V.2421, L.2428, I.2431, K.2432, V.2434, T.2435, R.2436 Ligands: PLX.24, PLX.25 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.2421, B:L.2428, B:I.2431, B:V.2434, B:T.2435 Salt bridges: B:K.2432 PLX.27: 11 residues within 4Å: Chain B: F.2455, V.2458, F.2462, F.2463, P.2561, L.2562, A.2565, I.2568, Y.2569, L.2572 Ligands: PLX.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.2455, B:V.2458, B:F.2462, B:F.2462, B:F.2463, B:L.2562, B:A.2565, B:I.2568, B:Y.2569 PLX.34: 11 residues within 4Å: Chain C: F.2455, V.2458, F.2462, F.2463, P.2561, L.2562, A.2565, I.2568, Y.2569, L.2572 Ligands: PLX.46 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.2455, C:V.2458, C:F.2462, C:F.2462, C:F.2463, C:L.2562, C:A.2565, C:I.2568, C:Y.2569 PLX.35: 8 residues within 4Å: Chain A: F.2563, A.2564, I.2568, L.2571 Chain C: L.2532, M.2533, V.2536 Ligands: PLX.8 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:A.2564, A:I.2568, A:L.2571, C:V.2536 PLX.36: 5 residues within 4Å: Chain C: R.2439 Chain D: F.2281, N.2282, V.2285, L.2420 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.2281, D:V.2285 Salt bridges: C:R.2439 PLX.37: 9 residues within 4Å: Chain A: L.2454, V.2458, L.2461, F.2462 Chain C: H.2409, F.2411, F.2412, S.2414, L.2415 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.2454, A:V.2458, A:L.2461, A:F.2462, C:F.2411, C:L.2415 PLX.38: 8 residues within 4Å: Chain C: V.2434, T.2435, R.2436, G.2438, R.2439, I.2441, I.2442 Ligands: PLX.40 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.2434, C:I.2441, C:I.2442 Hydrogen bonds: C:G.2438 PLX.39: 10 residues within 4Å: Chain C: V.2390, E.2391, L.2393, Y.2394, L.2397, F.2418, Y.2422, E.2425, L.2428 Ligands: PLX.40 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.2390, C:V.2390, C:E.2391, C:L.2393, C:Y.2394, C:L.2397, C:L.2397, C:F.2418, C:F.2418, C:L.2428 Salt bridges: C:E.2425 pi-Cation interactions: C:Y.2422 PLX.40: 9 residues within 4Å: Chain C: V.2421, L.2428, I.2431, K.2432, V.2434, T.2435, R.2436 Ligands: PLX.38, PLX.39 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.2421, C:L.2428, C:I.2431, C:V.2434, C:T.2435 Salt bridges: C:K.2432 PLX.46: 7 residues within 4Å: Chain C: F.2563, A.2564, I.2568, L.2571 Chain D: L.2532, M.2533 Ligands: PLX.34 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.2571 PLX.47: 5 residues within 4Å: Chain B: F.2281, N.2282, V.2285, L.2420 Chain D: R.2439 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:F.2281, B:V.2285 Salt bridges: D:R.2439 PLX.48: 9 residues within 4Å: Chain C: L.2454, V.2458, L.2461, F.2462 Chain D: H.2409, F.2411, F.2412, S.2414, L.2415 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.2454, C:V.2458, C:F.2462, D:F.2411, D:F.2412, D:L.2415 Salt bridges: D:H.2409 PLX.49: 8 residues within 4Å: Chain D: V.2434, T.2435, R.2436, G.2438, R.2439, I.2441, I.2442 Ligands: PLX.51 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.2434, D:I.2441, D:I.2442 PLX.50: 10 residues within 4Å: Chain D: V.2390, E.2391, L.2393, Y.2394, L.2397, F.2418, Y.2422, E.2425, L.2428 Ligands: PLX.51 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:V.2390, D:E.2391, D:L.2393, D:Y.2394, D:L.2397, D:F.2418, D:F.2418, D:L.2428 Salt bridges: D:E.2425 pi-Cation interactions: D:Y.2422 PLX.51: 9 residues within 4Å: Chain D: V.2421, L.2428, I.2431, K.2432, V.2434, T.2435, R.2436 Ligands: PLX.49, PLX.50 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.2421, D:L.2428, D:I.2431, D:V.2434, D:T.2435 Salt bridges: D:K.2432 PLX.52: 11 residues within 4Å: Chain D: F.2455, V.2458, F.2462, F.2463, P.2561, L.2562, A.2565, I.2568, Y.2569, L.2572 Ligands: PLX.21 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.2455, D:V.2458, D:F.2462, D:F.2462, D:F.2463, D:L.2562, D:A.2565, D:I.2568, D:Y.2569

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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