SMTL ID : 6o9u.1

KirBac3.1 at a resolution of 2 Angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

12 x TMO: trimethylamine oxide(Non-covalent)

TMO.1: 19 residues within 4Å: Chain A: Y.132, A.133, T.136, Q.252 Chain C: Y.132, T.136, F.250, A.251, Q.252 Ligands: K.9, K.10, K.26, K.27, TMO.35, K.43, K.44, TMO.52, K.60, K.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.136 TMO.2: 8 residues within 4Å: Chain A: I.172, E.173, D.175, R.204, T.244, G.245, H.246, N.253 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.175, A:T.244 Water bridges: A:T.244 Salt bridges: A:D.175 TMO.3: 5 residues within 4Å: Chain A: H.177, D.197, L.198, T.199, S.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.197 Water bridges: A:H.177, A:L.200 Salt bridges: A:D.197 TMO.18: 19 residues within 4Å: Chain B: Y.132, A.133, T.136, Q.252 Chain D: Y.132, T.136, F.250, A.251, Q.252 Ligands: K.9, K.10, K.26, K.27, TMO.35, K.43, K.44, TMO.52, K.60, K.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.136 TMO.19: 8 residues within 4Å: Chain B: I.172, E.173, D.175, R.204, T.244, G.245, H.246, N.253 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.175, B:T.244 Water bridges: B:T.244 Salt bridges: B:D.175 TMO.20: 5 residues within 4Å: Chain B: H.177, D.197, L.198, T.199, S.203 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.197 Water bridges: B:H.177, B:L.200 Salt bridges: B:D.197 TMO.35: 19 residues within 4Å: Chain B: Y.132, T.136, F.250, A.251, Q.252 Chain C: Y.132, A.133, T.136, Q.252 Ligands: TMO.1, K.9, K.10, TMO.18, K.26, K.27, K.43, K.44, K.60, K.61 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.136 TMO.36: 8 residues within 4Å: Chain C: I.172, E.173, D.175, R.204, T.244, G.245, H.246, N.253 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.175, C:T.244 Water bridges: C:T.244 Salt bridges: C:D.175 TMO.37: 5 residues within 4Å: Chain C: H.177, D.197, L.198, T.199, S.203 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.197 Water bridges: C:H.177, C:L.200 Salt bridges: C:D.197 TMO.52: 19 residues within 4Å: Chain A: Y.132, T.136, F.250, A.251, Q.252 Chain D: Y.132, A.133, T.136, Q.252 Ligands: TMO.1, K.9, K.10, TMO.18, K.26, K.27, K.43, K.44, K.60, K.61 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.136 TMO.53: 8 residues within 4Å: Chain D: I.172, E.173, D.175, R.204, T.244, G.245, H.246, N.253 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.175, D:T.244 Water bridges: D:T.244 Salt bridges: D:D.175 TMO.54: 5 residues within 4Å: Chain D: H.177, D.197, L.198, T.199, S.203 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.197 Water bridges: D:H.177, D:L.200 Salt bridges: D:D.197

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

K.4: 7 residues within 4Å: Chain A: G.100 Chain B: G.100 Chain C: G.100 Chain D: G.100 Ligands: K.21, K.38, K.55 Ligand excluded by PLIP K.5: 19 residues within 4Å: Chain A: G.98, Y.99, G.100 Chain B: G.98, Y.99, G.100 Chain C: G.98, Y.99, G.100 Chain D: G.98, Y.99, G.100 Ligands: K.6, K.22, K.23, K.39, K.40, K.56, K.57 Ligand excluded by PLIP K.6: 19 residues within 4Å: Chain A: I.97, G.98 Chain B: I.97, G.98 Chain C: I.97, G.98 Chain D: I.97, G.98 Ligands: K.5, K.7, K.22, K.23, K.24, K.39, K.40, K.41, K.56, K.57, K.58 Ligand excluded by PLIP K.7: 19 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.6, BA.13, K.23, K.24, BA.30, K.40, K.41, BA.47, K.57, K.58, BA.64 Ligand excluded by PLIP K.8: 3 residues within 4Å: Ligands: K.25, K.42, K.59 Ligand excluded by PLIP K.9: 15 residues within 4Å: Chain A: Y.132 Chain B: Y.132 Chain C: Y.132 Chain D: Y.132 Ligands: TMO.1, K.10, TMO.18, K.26, K.27, TMO.35, K.43, K.44, TMO.52, K.60, K.61 Ligand excluded by PLIP K.10: 11 residues within 4Å: Ligands: TMO.1, K.9, TMO.18, K.26, K.27, TMO.35, K.43, K.44, TMO.52, K.60, K.61 Ligand excluded by PLIP K.11: 6 residues within 4Å: Chain A: T.96, M.121, L.124 Chain C: L.124 Ligands: K.12, K.46 Ligand excluded by PLIP K.12: 7 residues within 4Å: Chain A: A.95, T.96, L.124 Chain D: T.96, M.121 Ligands: K.11, K.62 Ligand excluded by PLIP K.21: 7 residues within 4Å: Chain A: G.100 Chain B: G.100 Chain C: G.100 Chain D: G.100 Ligands: K.4, K.38, K.55 Ligand excluded by PLIP K.22: 19 residues within 4Å: Chain A: G.98, Y.99, G.100 Chain B: G.98, Y.99, G.100 Chain C: G.98, Y.99, G.100 Chain D: G.98, Y.99, G.100 Ligands: K.5, K.6, K.23, K.39, K.40, K.56, K.57 Ligand excluded by PLIP K.23: 19 residues within 4Å: Chain A: I.97, G.98 Chain B: I.97, G.98 Chain C: I.97, G.98 Chain D: I.97, G.98 Ligands: K.5, K.6, K.7, K.22, K.24, K.39, K.40, K.41, K.56, K.57, K.58 Ligand excluded by PLIP K.24: 19 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.6, K.7, BA.13, K.23, BA.30, K.40, K.41, BA.47, K.57, K.58, BA.64 Ligand excluded by PLIP K.25: 3 residues within 4Å: Ligands: K.8, K.42, K.59 Ligand excluded by PLIP K.26: 15 residues within 4Å: Chain A: Y.132 Chain B: Y.132 Chain C: Y.132 Chain D: Y.132 Ligands: TMO.1, K.9, K.10, TMO.18, K.27, TMO.35, K.43, K.44, TMO.52, K.60, K.61 Ligand excluded by PLIP K.27: 11 residues within 4Å: Ligands: TMO.1, K.9, K.10, TMO.18, K.26, TMO.35, K.43, K.44, TMO.52, K.60, K.61 Ligand excluded by PLIP K.28: 6 residues within 4Å: Chain B: T.96, M.121, L.124 Chain D: L.124 Ligands: K.29, K.63 Ligand excluded by PLIP K.29: 7 residues within 4Å: Chain B: A.95, T.96, L.124 Chain C: T.96, M.121 Ligands: K.28, K.45 Ligand excluded by PLIP K.38: 7 residues within 4Å: Chain A: G.100 Chain B: G.100 Chain C: G.100 Chain D: G.100 Ligands: K.4, K.21, K.55 Ligand excluded by PLIP K.39: 19 residues within 4Å: Chain A: G.98, Y.99, G.100 Chain B: G.98, Y.99, G.100 Chain C: G.98, Y.99, G.100 Chain D: G.98, Y.99, G.100 Ligands: K.5, K.6, K.22, K.23, K.40, K.56, K.57 Ligand excluded by PLIP K.40: 19 residues within 4Å: Chain A: I.97, G.98 Chain B: I.97, G.98 Chain C: I.97, G.98 Chain D: I.97, G.98 Ligands: K.5, K.6, K.7, K.22, K.23, K.24, K.39, K.41, K.56, K.57, K.58 Ligand excluded by PLIP K.41: 19 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.6, K.7, BA.13, K.23, K.24, BA.30, K.40, BA.47, K.57, K.58, BA.64 Ligand excluded by PLIP K.42: 3 residues within 4Å: Ligands: K.8, K.25, K.59 Ligand excluded by PLIP K.43: 15 residues within 4Å: Chain A: Y.132 Chain B: Y.132 Chain C: Y.132 Chain D: Y.132 Ligands: TMO.1, K.9, K.10, TMO.18, K.26, K.27, TMO.35, K.44, TMO.52, K.60, K.61 Ligand excluded by PLIP K.44: 11 residues within 4Å: Ligands: TMO.1, K.9, K.10, TMO.18, K.26, K.27, TMO.35, K.43, TMO.52, K.60, K.61 Ligand excluded by PLIP K.45: 6 residues within 4Å: Chain B: L.124 Chain C: T.96, M.121, L.124 Ligands: K.29, K.46 Ligand excluded by PLIP K.46: 7 residues within 4Å: Chain A: T.96, M.121 Chain C: A.95, T.96, L.124 Ligands: K.11, K.45 Ligand excluded by PLIP K.55: 7 residues within 4Å: Chain A: G.100 Chain B: G.100 Chain C: G.100 Chain D: G.100 Ligands: K.4, K.21, K.38 Ligand excluded by PLIP K.56: 19 residues within 4Å: Chain A: G.98, Y.99, G.100 Chain B: G.98, Y.99, G.100 Chain C: G.98, Y.99, G.100 Chain D: G.98, Y.99, G.100 Ligands: K.5, K.6, K.22, K.23, K.39, K.40, K.57 Ligand excluded by PLIP K.57: 19 residues within 4Å: Chain A: I.97, G.98 Chain B: I.97, G.98 Chain C: I.97, G.98 Chain D: I.97, G.98 Ligands: K.5, K.6, K.7, K.22, K.23, K.24, K.39, K.40, K.41, K.56, K.58 Ligand excluded by PLIP K.58: 19 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.6, K.7, BA.13, K.23, K.24, BA.30, K.40, K.41, BA.47, K.57, BA.64 Ligand excluded by PLIP K.59: 3 residues within 4Å: Ligands: K.8, K.25, K.42 Ligand excluded by PLIP K.60: 15 residues within 4Å: Chain A: Y.132 Chain B: Y.132 Chain C: Y.132 Chain D: Y.132 Ligands: TMO.1, K.9, K.10, TMO.18, K.26, K.27, TMO.35, K.43, K.44, TMO.52, K.61 Ligand excluded by PLIP K.61: 11 residues within 4Å: Ligands: TMO.1, K.9, K.10, TMO.18, K.26, K.27, TMO.35, K.43, K.44, TMO.52, K.60 Ligand excluded by PLIP K.62: 6 residues within 4Å: Chain A: L.124 Chain D: T.96, M.121, L.124 Ligands: K.12, K.63 Ligand excluded by PLIP K.63: 7 residues within 4Å: Chain B: T.96, M.121 Chain D: A.95, T.96, L.124 Ligands: K.28, K.62 Ligand excluded by PLIP

4 x BA: BARIUM ION(Non-covalent)

BA.13: 11 residues within 4Å: Chain A: T.96 Chain B: T.96 Chain C: T.96 Chain D: T.96 Ligands: K.7, K.24, BA.30, K.41, BA.47, K.58, BA.64 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:T.96, D:T.96, B:T.96, C:T.96 BA.30: 11 residues within 4Å: Chain A: T.96 Chain B: T.96 Chain C: T.96 Chain D: T.96 Ligands: K.7, BA.13, K.24, K.41, BA.47, K.58, BA.64 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:T.96, D:T.96, B:T.96, C:T.96 BA.47: 11 residues within 4Å: Chain A: T.96 Chain B: T.96 Chain C: T.96 Chain D: T.96 Ligands: K.7, BA.13, K.24, BA.30, K.41, K.58, BA.64 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:T.96, D:T.96, B:T.96, A:T.96 BA.64: 11 residues within 4Å: Chain A: T.96 Chain B: T.96 Chain C: T.96 Chain D: T.96 Ligands: K.7, BA.13, K.24, BA.30, K.41, BA.47, K.58 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:T.96, D:T.96, B:T.96, A:T.96

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 5 residues within 4Å: Chain A: T.201, R.202, M.215 Chain D: R.194 Ligands: PCW.16 Ligand excluded by PLIP CL.31: 5 residues within 4Å: Chain B: T.201, R.202, M.215 Chain C: R.194 Ligands: PCW.33 Ligand excluded by PLIP CL.48: 5 residues within 4Å: Chain A: R.194 Chain C: T.201, R.202, M.215 Ligands: PCW.50 Ligand excluded by PLIP CL.65: 5 residues within 4Å: Chain B: R.194 Chain D: T.201, R.202, M.215 Ligands: PCW.67 Ligand excluded by PLIP

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

PCW.15: 13 residues within 4Å: Chain A: L.118, M.121, L.122 Chain C: I.53, L.56, Y.57, T.60, M.94, C.119, G.120, G.123, L.124, A.127 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:L.56, C:T.60, C:L.124, C:A.127, A:L.118, A:M.121, A:L.122 PCW.16: 10 residues within 4Å: Chain A: F.153, M.160, T.213, M.215 Chain D: M.190, F.192, R.193, R.194 Ligands: CL.14, Z3P.17 No protein-ligand interaction detected (PLIP) PCW.32: 13 residues within 4Å: Chain B: L.118, M.121, L.122 Chain D: I.53, L.56, Y.57, T.60, M.94, C.119, G.120, G.123, L.124, A.127 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:L.118, B:M.121, B:L.122, D:L.56, D:T.60, D:L.124, D:A.127 PCW.33: 10 residues within 4Å: Chain B: F.153, M.160, T.213, M.215 Chain C: M.190, F.192, R.193, R.194 Ligands: CL.31, Z3P.34 No protein-ligand interaction detected (PLIP) PCW.49: 13 residues within 4Å: Chain B: I.53, L.56, Y.57, T.60, M.94, C.119, G.120, G.123, L.124, A.127 Chain C: L.118, M.121, L.122 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.118, C:M.121, C:L.122, B:L.56, B:T.60, B:L.124, B:A.127 PCW.50: 10 residues within 4Å: Chain A: M.190, F.192, R.193, R.194 Chain C: F.153, M.160, T.213, M.215 Ligands: CL.48, Z3P.51 No protein-ligand interaction detected (PLIP) PCW.66: 13 residues within 4Å: Chain A: I.53, L.56, Y.57, T.60, M.94, C.119, G.120, G.123, L.124, A.127 Chain D: L.118, M.121, L.122 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:L.118, D:M.121, D:L.122, A:L.56, A:T.60, A:L.124, A:A.127 PCW.67: 10 residues within 4Å: Chain B: M.190, F.192, R.193, R.194 Chain D: F.153, M.160, T.213, M.215 Ligands: CL.65, Z3P.68 No protein-ligand interaction detected (PLIP)

4 x Z3P: 3,3',3''-phosphoryltripropanoic acid(Non-covalent)

Z3P.17: 17 residues within 4Å: Chain A: S.205, I.207, F.208, S.209, L.210, S.211, W.212, T.213, F.275, R.283 Chain D: I.14, I.23, V.181, R.193, R.194, F.195 Ligands: PCW.16 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.275 Hydrogen bonds: A:S.209, A:L.210, A:S.211, A:T.213, A:T.213 Water bridges: A:T.213, A:T.213, D:R.193, D:R.193 Salt bridges: A:R.283 Z3P.34: 17 residues within 4Å: Chain B: S.205, I.207, F.208, S.209, L.210, S.211, W.212, T.213, F.275, R.283 Chain C: I.14, I.23, V.181, R.193, R.194, F.195 Ligands: PCW.33 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.275 Hydrogen bonds: B:S.209, B:L.210, B:S.211, B:T.213, B:T.213 Water bridges: B:T.213, B:T.213, C:R.193, C:R.193 Salt bridges: B:R.283 Z3P.51: 17 residues within 4Å: Chain A: I.14, I.23, V.181, R.193, R.194, F.195 Chain C: S.205, I.207, F.208, S.209, L.210, S.211, W.212, T.213, F.275, R.283 Ligands: PCW.50 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.275 Hydrogen bonds: C:S.209, C:L.210, C:S.211, C:T.213, C:T.213 Water bridges: C:T.213, C:T.213, A:R.193, A:R.193 Salt bridges: C:R.283 Z3P.68: 17 residues within 4Å: Chain B: I.14, I.23, V.181, R.193, R.194, F.195 Chain D: S.205, I.207, F.208, S.209, L.210, S.211, W.212, T.213, F.275, R.283 Ligands: PCW.67 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.275 Hydrogen bonds: D:S.209, D:L.210, D:S.211, D:T.213, D:T.213 Water bridges: D:T.213, D:T.213, B:R.193, B:R.193 Salt bridges: D:R.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Black, K.A. et al., A constricted opening in Kir channels does not impede potassium conduction. Nat Commun (2020)

Release Date

2020-05-27

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

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