SMTL ID : 8yfc.1

Human PIEZO1-A1988V-MDFIC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

15 x D12: DODECANE(Non-covalent)

D12.1: 7 residues within 4Å: Chain A: F.2104, G.2108, L.2111 Chain E: C.240 Ligands: L9Q.4, D12.13, D12.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.2111 D12.2: 4 residues within 4Å: Chain A: L.2178, F.2182 Ligands: D12.13, D12.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.2178, A:F.2182, A:F.2182 D12.5: 7 residues within 4Å: Chain B: F.2104, G.2108, L.2111 Chain F: C.240 Ligands: L9Q.7, D12.16, D12.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.2111 D12.6: 4 residues within 4Å: Chain B: L.2178, F.2182 Ligands: D12.16, D12.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.2178, B:F.2182, B:F.2182 D12.8: 7 residues within 4Å: Chain C: F.2104, G.2108, L.2111 Chain D: C.240 Ligands: L9Q.3, D12.10, D12.11 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.2111 D12.9: 4 residues within 4Å: Chain C: L.2178, F.2182 Ligands: D12.10, D12.11 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.2178, C:F.2182, C:F.2182 D12.10: 5 residues within 4Å: Chain D: C.236 Ligands: D12.8, D12.9, D12.11, D12.12 No protein-ligand interaction detected (PLIP) D12.11: 6 residues within 4Å: Chain C: L.2111 Chain D: C.243 Ligands: L9Q.3, D12.8, D12.9, D12.10 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.2111 D12.12: 3 residues within 4Å: Chain C: L.2178 Chain D: C.232 Ligands: D12.10 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.2178 D12.13: 5 residues within 4Å: Chain E: C.236 Ligands: D12.1, D12.2, D12.14, D12.15 No protein-ligand interaction detected (PLIP) D12.14: 6 residues within 4Å: Chain A: L.2111 Chain E: C.243 Ligands: D12.1, D12.2, L9Q.4, D12.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.2111 D12.15: 3 residues within 4Å: Chain A: L.2178 Chain E: C.232 Ligands: D12.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.2178 D12.16: 5 residues within 4Å: Chain F: C.236 Ligands: D12.5, D12.6, D12.17, D12.18 No protein-ligand interaction detected (PLIP) D12.17: 6 residues within 4Å: Chain B: L.2111 Chain F: C.243 Ligands: D12.5, D12.6, L9Q.7, D12.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.2111 D12.18: 3 residues within 4Å: Chain B: L.2178 Chain F: C.232 Ligands: D12.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.2178

3 x L9Q: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

L9Q.3: 14 residues within 4Å: Chain A: L.2449, K.2453, R.2456, S.2460 Chain C: G.2108, R.2110, L.2111, P.2113, I.2451, F.2454 Ligands: L9Q.4, L9Q.7, D12.8, D12.11 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:I.2451, C:F.2454, C:F.2454, A:L.2449, A:K.2453, A:K.2453 Salt bridges: C:R.2110, A:K.2453, A:K.2453, A:R.2456, A:R.2456 L9Q.4: 14 residues within 4Å: Chain A: G.2108, R.2110, L.2111, P.2113, I.2451, F.2454 Chain B: L.2449, K.2453, R.2456, S.2460 Ligands: D12.1, L9Q.3, L9Q.7, D12.14 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.2451, A:F.2454, A:F.2454, B:L.2449, B:K.2453, B:K.2453 Salt bridges: A:R.2110, B:K.2453, B:K.2453, B:R.2456, B:R.2456 L9Q.7: 14 residues within 4Å: Chain B: G.2108, R.2110, L.2111, P.2113, I.2451, F.2454 Chain C: L.2449, K.2453, R.2456, S.2460 Ligands: L9Q.3, L9Q.4, D12.5, D12.17 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.2449, C:K.2453, C:K.2453, B:I.2451, B:F.2454, B:F.2454 Salt bridges: C:K.2453, C:K.2453, C:R.2456, C:R.2456, B:R.2110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shan, Y. et al., Structure of human PIEZO1 and its slow inactivating channelopathy mutants. Elife (2024)

Release Date

2025-01-15

Peptides

Piezo-type mechanosensitive ion channel component 1: ABC
MyoD family inhibitor domain-containing protein: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

E
E

F
F

Piezo-type mechanosensitive ion channel component 1

MyoD family inhibitor domain-containing protein

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