- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.40 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
- 4 x 1N7: CHAPSO(Non-covalent)
1N7.3: 7 residues within 4Å:- Chain A: Q.119, M.120
- Chain C: P.132, L.135, S.136, A.139
- Ligands: PX4.34
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain A- Hydrophobic interactions: C:L.135, C:A.139, A:Q.119
- Hydrogen bonds: C:L.135, C:S.136
1N7.16: 7 residues within 4Å:- Chain B: Q.119, M.120
- Chain D: P.132, L.135, S.136, A.139
- Ligands: PX4.47
5 PLIP interactions:4 interactions with chain D, 1 interactions with chain B- Hydrophobic interactions: D:L.135, D:A.139, B:Q.119
- Hydrogen bonds: D:L.135, D:S.136
1N7.29: 7 residues within 4Å:- Chain B: P.132, L.135, S.136, A.139
- Chain C: Q.119, M.120
- Ligands: PX4.21
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain C- Hydrophobic interactions: B:L.135, B:A.139, C:Q.119
- Hydrogen bonds: B:L.135, B:S.136
1N7.42: 7 residues within 4Å:- Chain A: P.132, L.135, S.136, A.139
- Chain D: Q.119, M.120
- Ligands: PX4.8
5 PLIP interactions:1 interactions with chain D, 4 interactions with chain A- Hydrophobic interactions: D:Q.119, A:L.135, A:A.139
- Hydrogen bonds: A:L.135, A:S.136
- 32 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
PX4.4: 20 residues within 4Å:- Chain A: W.199, I.203, F.207
- Chain D: I.138, M.141, T.142, F.145, G.168, E.169, F.171, Y.172, F.175, M.178, M.213, L.216
- Ligands: PX4.18, PX4.24, LMT.40, PX4.46, PX4.47
Ligand excluded by PLIPPX4.5: 12 residues within 4Å:- Chain A: I.31, G.34, S.38, K.39, T.40
- Chain C: Y.146, T.166, L.167, G.168, F.171
- Ligands: PX4.11, PX4.17
Ligand excluded by PLIPPX4.6: 12 residues within 4Å:- Chain A: P.79, W.80, F.83, S.125, I.128, S.129, I.131, P.132
- Ligands: LMT.1, PX4.8, PX4.9, PX4.10
Ligand excluded by PLIPPX4.7: 5 residues within 4Å:- Chain A: I.101
- Chain C: Y.197, W.199
- Ligands: LMT.28, PX4.30
Ligand excluded by PLIPPX4.8: 5 residues within 4Å:- Chain A: L.135
- Ligands: PX4.6, PX4.9, PX4.30, 1N7.42
Ligand excluded by PLIPPX4.9: 5 residues within 4Å:- Chain A: S.129, P.132
- Ligands: PX4.6, PX4.8, PX4.10
Ligand excluded by PLIPPX4.10: 7 residues within 4Å:- Chain A: K.77, P.79, L.82, F.83, F.86
- Ligands: PX4.6, PX4.9
Ligand excluded by PLIPPX4.11: 4 residues within 4Å:- Chain A: T.40
- Chain B: Y.197
- Ligands: PX4.5, PX4.17
Ligand excluded by PLIPPX4.17: 20 residues within 4Å:- Chain B: W.199, I.203, F.207
- Chain C: I.138, M.141, T.142, F.145, G.168, E.169, F.171, Y.172, F.175, M.178, M.213, L.216
- Ligands: PX4.5, PX4.11, LMT.27, PX4.33, PX4.34
Ligand excluded by PLIPPX4.18: 12 residues within 4Å:- Chain B: I.31, G.34, S.38, K.39, T.40
- Chain D: Y.146, T.166, L.167, G.168, F.171
- Ligands: PX4.4, PX4.24
Ligand excluded by PLIPPX4.19: 12 residues within 4Å:- Chain B: P.79, W.80, F.83, S.125, I.128, S.129, I.131, P.132
- Ligands: LMT.14, PX4.21, PX4.22, PX4.23
Ligand excluded by PLIPPX4.20: 5 residues within 4Å:- Chain B: I.101
- Chain D: Y.197, W.199
- Ligands: LMT.41, PX4.43
Ligand excluded by PLIPPX4.21: 5 residues within 4Å:- Chain B: L.135
- Ligands: PX4.19, PX4.22, 1N7.29, PX4.43
Ligand excluded by PLIPPX4.22: 5 residues within 4Å:- Chain B: S.129, P.132
- Ligands: PX4.19, PX4.21, PX4.23
Ligand excluded by PLIPPX4.23: 7 residues within 4Å:- Chain B: K.77, P.79, L.82, F.83, F.86
- Ligands: PX4.19, PX4.22
Ligand excluded by PLIPPX4.24: 4 residues within 4Å:- Chain A: Y.197
- Chain B: T.40
- Ligands: PX4.4, PX4.18
Ligand excluded by PLIPPX4.30: 20 residues within 4Å:- Chain A: I.138, M.141, T.142, F.145, G.168, E.169, F.171, Y.172, F.175, M.178, M.213, L.216
- Chain C: W.199, I.203, F.207
- Ligands: LMT.1, PX4.7, PX4.8, PX4.44, PX4.50
Ligand excluded by PLIPPX4.31: 12 residues within 4Å:- Chain B: Y.146, T.166, L.167, G.168, F.171
- Chain C: I.31, G.34, S.38, K.39, T.40
- Ligands: PX4.37, PX4.43
Ligand excluded by PLIPPX4.32: 12 residues within 4Å:- Chain C: P.79, W.80, F.83, S.125, I.128, S.129, I.131, P.132
- Ligands: LMT.27, PX4.34, PX4.35, PX4.36
Ligand excluded by PLIPPX4.33: 5 residues within 4Å:- Chain B: Y.197, W.199
- Chain C: I.101
- Ligands: LMT.15, PX4.17
Ligand excluded by PLIPPX4.34: 5 residues within 4Å:- Chain C: L.135
- Ligands: 1N7.3, PX4.17, PX4.32, PX4.35
Ligand excluded by PLIPPX4.35: 5 residues within 4Å:- Chain C: S.129, P.132
- Ligands: PX4.32, PX4.34, PX4.36
Ligand excluded by PLIPPX4.36: 7 residues within 4Å:- Chain C: K.77, P.79, L.82, F.83, F.86
- Ligands: PX4.32, PX4.35
Ligand excluded by PLIPPX4.37: 4 residues within 4Å:- Chain C: T.40
- Chain D: Y.197
- Ligands: PX4.31, PX4.43
Ligand excluded by PLIPPX4.43: 20 residues within 4Å:- Chain B: I.138, M.141, T.142, F.145, G.168, E.169, F.171, Y.172, F.175, M.178, M.213, L.216
- Chain D: W.199, I.203, F.207
- Ligands: LMT.14, PX4.20, PX4.21, PX4.31, PX4.37
Ligand excluded by PLIPPX4.44: 12 residues within 4Å:- Chain A: Y.146, T.166, L.167, G.168, F.171
- Chain D: I.31, G.34, S.38, K.39, T.40
- Ligands: PX4.30, PX4.50
Ligand excluded by PLIPPX4.45: 12 residues within 4Å:- Chain D: P.79, W.80, F.83, S.125, I.128, S.129, I.131, P.132
- Ligands: LMT.40, PX4.47, PX4.48, PX4.49
Ligand excluded by PLIPPX4.46: 5 residues within 4Å:- Chain A: Y.197, W.199
- Chain D: I.101
- Ligands: LMT.2, PX4.4
Ligand excluded by PLIPPX4.47: 5 residues within 4Å:- Chain D: L.135
- Ligands: PX4.4, 1N7.16, PX4.45, PX4.48
Ligand excluded by PLIPPX4.48: 5 residues within 4Å:- Chain D: S.129, P.132
- Ligands: PX4.45, PX4.47, PX4.49
Ligand excluded by PLIPPX4.49: 7 residues within 4Å:- Chain D: K.77, P.79, L.82, F.83, F.86
- Ligands: PX4.45, PX4.48
Ligand excluded by PLIPPX4.50: 4 residues within 4Å:- Chain C: Y.197
- Chain D: T.40
- Ligands: PX4.30, PX4.44
Ligand excluded by PLIP- 8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)
CA.12: 6 residues within 4Å:- Chain A: Q.180
- Chain D: T.179
- Ligands: LMT.1, CA.38, LMT.40, CA.51
No protein-ligand interaction detected (PLIP)CA.13: 3 residues within 4Å:- Ligands: CA.26, CA.39, CA.52
No protein-ligand interaction detected (PLIP)CA.25: 6 residues within 4Å:- Chain B: Q.180
- Chain C: T.179
- Ligands: LMT.14, LMT.27, CA.38, CA.51
No protein-ligand interaction detected (PLIP)CA.26: 3 residues within 4Å:- Ligands: CA.13, CA.39, CA.52
No protein-ligand interaction detected (PLIP)CA.38: 6 residues within 4Å:- Chain A: T.179
- Chain C: Q.180
- Ligands: LMT.1, CA.12, CA.25, LMT.27
No protein-ligand interaction detected (PLIP)CA.39: 3 residues within 4Å:- Ligands: CA.13, CA.26, CA.52
No protein-ligand interaction detected (PLIP)CA.51: 6 residues within 4Å:- Chain B: T.179
- Chain D: Q.180
- Ligands: CA.12, LMT.14, CA.25, LMT.40
No protein-ligand interaction detected (PLIP)CA.52: 3 residues within 4Å:- Ligands: CA.13, CA.26, CA.39
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Irie, K. et al., The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel. Nat Commun (2023)
- Release Date
- 2023-07-26
- Peptides
- Ion transport protein: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.40 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
- 4 x 1N7: CHAPSO(Non-covalent)
- 32 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
- 8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Irie, K. et al., The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel. Nat Commun (2023)
- Release Date
- 2023-07-26
- Peptides
- Ion transport protein: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A - Membrane
-
We predict this structure to be a membrane protein.