SMTL ID : 7n9k.1

KirBac3.1 L124M mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-tetramer

Ligands

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

PCW.1: 11 residues within 4Å: Chain A: L.34, H.37, L.41, I.53, L.56, G.123, V.126, A.127, L.130 Chain C: F.135 Ligands: PCW.26 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.34, A:I.53, A:L.56, A:A.127 PCW.2: 9 residues within 4Å: Chain A: W.46, F.49, I.50, I.131, F.135 Chain D: H.37, L.122, V.126 Ligands: PCW.37 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:L.122, D:L.122, D:V.126, A:W.46, A:W.46, A:I.50, A:I.131 PCW.4: 10 residues within 4Å: Chain A: L.56, Y.57, T.60, F.64, M.94, C.119, G.120, G.123, M.124, A.127 No protein-ligand interaction detected (PLIP) PCW.13: 11 residues within 4Å: Chain B: L.34, H.37, L.41, I.53, L.56, G.123, V.126, A.127, L.130 Chain D: F.135 Ligands: PCW.38 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.34, B:I.53, B:L.56, B:A.127 PCW.14: 9 residues within 4Å: Chain B: W.46, F.49, I.50, I.131, F.135 Chain C: H.37, L.122, V.126 Ligands: PCW.25 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.122, C:L.122, C:V.126, B:W.46, B:W.46, B:I.50, B:I.131 PCW.16: 10 residues within 4Å: Chain B: L.56, Y.57, T.60, F.64, M.94, C.119, G.120, G.123, M.124, A.127 No protein-ligand interaction detected (PLIP) PCW.25: 11 residues within 4Å: Chain B: F.135 Chain C: L.34, H.37, L.41, I.53, L.56, G.123, V.126, A.127, L.130 Ligands: PCW.14 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.34, C:I.53, C:L.56, C:A.127 PCW.26: 9 residues within 4Å: Chain A: H.37, L.122, V.126 Chain C: W.46, F.49, I.50, I.131, F.135 Ligands: PCW.1 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.122, A:L.122, A:V.126, C:W.46, C:W.46, C:I.50, C:I.131 PCW.28: 10 residues within 4Å: Chain C: L.56, Y.57, T.60, F.64, M.94, C.119, G.120, G.123, M.124, A.127 No protein-ligand interaction detected (PLIP) PCW.37: 11 residues within 4Å: Chain A: F.135 Chain D: L.34, H.37, L.41, I.53, L.56, G.123, V.126, A.127, L.130 Ligands: PCW.2 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.34, D:I.53, D:L.56, D:A.127 PCW.38: 9 residues within 4Å: Chain B: H.37, L.122, V.126 Chain D: W.46, F.49, I.50, I.131, F.135 Ligands: PCW.13 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:W.46, D:W.46, D:I.50, D:I.131, B:L.122, B:L.122, B:V.126 PCW.40: 10 residues within 4Å: Chain D: L.56, Y.57, T.60, F.64, M.94, C.119, G.120, G.123, M.124, A.127 No protein-ligand interaction detected (PLIP)

4 x TMO: trimethylamine oxide(Non-covalent)

TMO.3: 9 residues within 4Å: Chain A: Y.132, A.133, T.136 Chain C: Y.132, F.250, A.251, Q.252 Ligands: TMO.27, TMO.39 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.132 TMO.15: 9 residues within 4Å: Chain B: Y.132, A.133, T.136 Chain D: Y.132, F.250, A.251, Q.252 Ligands: TMO.27, TMO.39 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.132 TMO.27: 9 residues within 4Å: Chain B: Y.132, F.250, A.251, Q.252 Chain C: Y.132, A.133, T.136 Ligands: TMO.3, TMO.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.132 TMO.39: 9 residues within 4Å: Chain A: Y.132, F.250, A.251, Q.252 Chain D: Y.132, A.133, T.136 Ligands: TMO.3, TMO.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.132

4 x OCT: N-OCTANE(Non-covalent)

OCT.5: 11 residues within 4Å: Chain A: M.124, A.128 Chain D: M.121, M.124, A.125, A.128 Ligands: K.12, OCT.17, OCT.29, OCT.41, K.47 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:M.124, D:M.121, D:A.125, D:A.128 OCT.17: 11 residues within 4Å: Chain B: M.124, A.128 Chain C: M.121, M.124, A.125, A.128 Ligands: OCT.5, K.24, OCT.29, K.35, OCT.41 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:M.121, C:A.125, C:A.128, B:M.124 OCT.29: 11 residues within 4Å: Chain A: M.121, M.124, A.125, A.128 Chain C: M.124, A.128 Ligands: OCT.5, K.11, OCT.17, K.36, OCT.41 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:M.124, A:M.121, A:A.125, A:A.128 OCT.41: 11 residues within 4Å: Chain B: M.121, M.124, A.125, A.128 Chain D: M.124, A.128 Ligands: OCT.5, OCT.17, K.23, OCT.29, K.48 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:M.121, B:A.125, B:A.128, D:M.124

28 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.6: 11 residues within 4Å: Chain A: G.98, Y.99 Chain B: G.98, Y.99 Chain C: G.98, Y.99 Chain D: G.98, Y.99 Ligands: K.18, K.30, K.42 Ligand excluded by PLIP K.7: 15 residues within 4Å: Chain A: T.96, I.97 Chain B: T.96, I.97 Chain C: T.96, I.97 Chain D: T.96, I.97 Ligands: K.8, K.19, K.20, K.31, K.32, K.43, K.44 Ligand excluded by PLIP K.8: 11 residues within 4Å: Chain A: T.96 Chain B: T.96 Chain C: T.96 Chain D: T.96 Ligands: K.7, K.19, K.20, K.31, K.32, K.43, K.44 Ligand excluded by PLIP K.9: 7 residues within 4Å: Ligands: K.11, K.21, K.23, K.33, K.35, K.45, K.47 Ligand excluded by PLIP K.10: 3 residues within 4Å: Ligands: K.22, K.34, K.46 Ligand excluded by PLIP K.11: 7 residues within 4Å: Chain A: T.96, M.124 Ligands: K.9, K.21, OCT.29, K.33, K.45 Ligand excluded by PLIP K.12: 6 residues within 4Å: Chain A: A.128, Y.132 Chain D: A.128 Ligands: OCT.5, K.36, K.48 Ligand excluded by PLIP K.18: 11 residues within 4Å: Chain A: G.98, Y.99 Chain B: G.98, Y.99 Chain C: G.98, Y.99 Chain D: G.98, Y.99 Ligands: K.6, K.30, K.42 Ligand excluded by PLIP K.19: 15 residues within 4Å: Chain A: T.96, I.97 Chain B: T.96, I.97 Chain C: T.96, I.97 Chain D: T.96, I.97 Ligands: K.7, K.8, K.20, K.31, K.32, K.43, K.44 Ligand excluded by PLIP K.20: 11 residues within 4Å: Chain A: T.96 Chain B: T.96 Chain C: T.96 Chain D: T.96 Ligands: K.7, K.8, K.19, K.31, K.32, K.43, K.44 Ligand excluded by PLIP K.21: 7 residues within 4Å: Ligands: K.9, K.11, K.23, K.33, K.35, K.45, K.47 Ligand excluded by PLIP K.22: 3 residues within 4Å: Ligands: K.10, K.34, K.46 Ligand excluded by PLIP K.23: 7 residues within 4Å: Chain B: T.96, M.124 Ligands: K.9, K.21, K.33, OCT.41, K.45 Ligand excluded by PLIP K.24: 6 residues within 4Å: Chain B: A.128, Y.132 Chain C: A.128 Ligands: OCT.17, K.36, K.48 Ligand excluded by PLIP K.30: 11 residues within 4Å: Chain A: G.98, Y.99 Chain B: G.98, Y.99 Chain C: G.98, Y.99 Chain D: G.98, Y.99 Ligands: K.6, K.18, K.42 Ligand excluded by PLIP K.31: 15 residues within 4Å: Chain A: T.96, I.97 Chain B: T.96, I.97 Chain C: T.96, I.97 Chain D: T.96, I.97 Ligands: K.7, K.8, K.19, K.20, K.32, K.43, K.44 Ligand excluded by PLIP K.32: 11 residues within 4Å: Chain A: T.96 Chain B: T.96 Chain C: T.96 Chain D: T.96 Ligands: K.7, K.8, K.19, K.20, K.31, K.43, K.44 Ligand excluded by PLIP K.33: 7 residues within 4Å: Ligands: K.9, K.11, K.21, K.23, K.35, K.45, K.47 Ligand excluded by PLIP K.34: 3 residues within 4Å: Ligands: K.10, K.22, K.46 Ligand excluded by PLIP K.35: 7 residues within 4Å: Chain C: T.96, M.124 Ligands: K.9, OCT.17, K.21, K.33, K.45 Ligand excluded by PLIP K.36: 6 residues within 4Å: Chain A: A.128 Chain C: A.128, Y.132 Ligands: K.12, K.24, OCT.29 Ligand excluded by PLIP K.42: 11 residues within 4Å: Chain A: G.98, Y.99 Chain B: G.98, Y.99 Chain C: G.98, Y.99 Chain D: G.98, Y.99 Ligands: K.6, K.18, K.30 Ligand excluded by PLIP K.43: 15 residues within 4Å: Chain A: T.96, I.97 Chain B: T.96, I.97 Chain C: T.96, I.97 Chain D: T.96, I.97 Ligands: K.7, K.8, K.19, K.20, K.31, K.32, K.44 Ligand excluded by PLIP K.44: 11 residues within 4Å: Chain A: T.96 Chain B: T.96 Chain C: T.96 Chain D: T.96 Ligands: K.7, K.8, K.19, K.20, K.31, K.32, K.43 Ligand excluded by PLIP K.45: 7 residues within 4Å: Ligands: K.9, K.11, K.21, K.23, K.33, K.35, K.47 Ligand excluded by PLIP K.46: 3 residues within 4Å: Ligands: K.10, K.22, K.34 Ligand excluded by PLIP K.47: 7 residues within 4Å: Chain D: T.96, M.124 Ligands: OCT.5, K.9, K.21, K.33, K.45 Ligand excluded by PLIP K.48: 6 residues within 4Å: Chain B: A.128 Chain D: A.128, Y.132 Ligands: K.12, K.24, OCT.41 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, R. et al., Ion currents through Kir potassium channels are gated by anionic lipids. Nat Commun (2022)

Release Date

2021-12-29

Peptides

Inward rectifier potassium channel Kirbac3.1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Membrane

We predict this structure to be a membrane protein.
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Inward rectifier potassium channel Kirbac3.1