- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.70 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
- 4 x 1N7: CHAPSO(Non-covalent)
1N7.2: 9 residues within 4Å:- Chain A: Q.119, M.120
- Chain C: P.132, G.133, L.135, S.136, D.223
- Ligands: PX4.31, PX4.32
3 PLIP interactions:1 interactions with chain C, 2 interactions with chain A- Hydrophobic interactions: C:L.135, A:Q.119, A:Q.119
1N7.14: 9 residues within 4Å:- Chain B: Q.119, M.120
- Chain D: P.132, G.133, L.135, S.136, D.223
- Ligands: PX4.43, PX4.44
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain B- Hydrophobic interactions: D:L.135, B:Q.119, B:Q.119
1N7.26: 9 residues within 4Å:- Chain B: P.132, G.133, L.135, S.136, D.223
- Chain C: Q.119, M.120
- Ligands: PX4.19, PX4.20
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: C:Q.119, C:Q.119, B:L.135
1N7.38: 9 residues within 4Å:- Chain A: P.132, G.133, L.135, S.136, D.223
- Chain D: Q.119, M.120
- Ligands: PX4.7, PX4.8
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain D- Hydrophobic interactions: A:L.135, D:Q.119, D:Q.119
- 32 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)
PX4.3: 19 residues within 4Å:- Chain A: M.192, P.196, W.199, F.207
- Chain D: I.131, I.138, M.141, F.145, G.168, E.169, F.171, Y.172, F.175, M.213, L.216
- Ligands: PX4.16, PX4.22, PX4.43, LMT.48
Ligand excluded by PLIPPX4.4: 15 residues within 4Å:- Chain A: I.26, V.27, I.31, G.34, S.38, K.39, T.40, L.113
- Chain C: L.143, Y.146, T.166, L.167, G.168
- Ligands: PX4.10, PX4.15
Ligand excluded by PLIPPX4.5: 13 residues within 4Å:- Chain A: P.79, W.80, F.83, S.125, A.126, L.127, I.128, S.129, I.131, P.132
- Ligands: PX4.7, PX4.8, PX4.9
Ligand excluded by PLIPPX4.6: 7 residues within 4Å:- Chain C: Y.197, W.199, I.203, P.204
- Ligands: PX4.7, PX4.8, LMT.25
Ligand excluded by PLIPPX4.7: 5 residues within 4Å:- Ligands: PX4.5, PX4.6, PX4.8, PX4.27, 1N7.38
Ligand excluded by PLIPPX4.8: 5 residues within 4Å:- Ligands: PX4.5, PX4.6, PX4.7, PX4.9, 1N7.38
Ligand excluded by PLIPPX4.9: 10 residues within 4Å:- Chain A: K.77, P.79, W.80, L.82, F.83, F.86, I.90, S.125
- Ligands: PX4.5, PX4.8
Ligand excluded by PLIPPX4.10: 3 residues within 4Å:- Chain B: Y.197
- Ligands: PX4.4, PX4.15
Ligand excluded by PLIPPX4.15: 19 residues within 4Å:- Chain B: M.192, P.196, W.199, F.207
- Chain C: I.131, I.138, M.141, F.145, G.168, E.169, F.171, Y.172, F.175, M.213, L.216
- Ligands: PX4.4, PX4.10, PX4.31, LMT.36
Ligand excluded by PLIPPX4.16: 15 residues within 4Å:- Chain B: I.26, V.27, I.31, G.34, S.38, K.39, T.40, L.113
- Chain D: L.143, Y.146, T.166, L.167, G.168
- Ligands: PX4.3, PX4.22
Ligand excluded by PLIPPX4.17: 13 residues within 4Å:- Chain B: P.79, W.80, F.83, S.125, A.126, L.127, I.128, S.129, I.131, P.132
- Ligands: PX4.19, PX4.20, PX4.21
Ligand excluded by PLIPPX4.18: 7 residues within 4Å:- Chain D: Y.197, W.199, I.203, P.204
- Ligands: PX4.19, PX4.20, LMT.37
Ligand excluded by PLIPPX4.19: 5 residues within 4Å:- Ligands: PX4.17, PX4.18, PX4.20, 1N7.26, PX4.39
Ligand excluded by PLIPPX4.20: 5 residues within 4Å:- Ligands: PX4.17, PX4.18, PX4.19, PX4.21, 1N7.26
Ligand excluded by PLIPPX4.21: 10 residues within 4Å:- Chain B: K.77, P.79, W.80, L.82, F.83, F.86, I.90, S.125
- Ligands: PX4.17, PX4.20
Ligand excluded by PLIPPX4.22: 3 residues within 4Å:- Chain A: Y.197
- Ligands: PX4.3, PX4.16
Ligand excluded by PLIPPX4.27: 19 residues within 4Å:- Chain A: I.131, I.138, M.141, F.145, G.168, E.169, F.171, Y.172, F.175, M.213, L.216
- Chain C: M.192, P.196, W.199, F.207
- Ligands: PX4.7, LMT.12, PX4.40, PX4.46
Ligand excluded by PLIPPX4.28: 15 residues within 4Å:- Chain B: L.143, Y.146, T.166, L.167, G.168
- Chain C: I.26, V.27, I.31, G.34, S.38, K.39, T.40, L.113
- Ligands: PX4.34, PX4.39
Ligand excluded by PLIPPX4.29: 13 residues within 4Å:- Chain C: P.79, W.80, F.83, S.125, A.126, L.127, I.128, S.129, I.131, P.132
- Ligands: PX4.31, PX4.32, PX4.33
Ligand excluded by PLIPPX4.30: 7 residues within 4Å:- Chain B: Y.197, W.199, I.203, P.204
- Ligands: LMT.13, PX4.31, PX4.32
Ligand excluded by PLIPPX4.31: 5 residues within 4Å:- Ligands: 1N7.2, PX4.15, PX4.29, PX4.30, PX4.32
Ligand excluded by PLIPPX4.32: 5 residues within 4Å:- Ligands: 1N7.2, PX4.29, PX4.30, PX4.31, PX4.33
Ligand excluded by PLIPPX4.33: 10 residues within 4Å:- Chain C: K.77, P.79, W.80, L.82, F.83, F.86, I.90, S.125
- Ligands: PX4.29, PX4.32
Ligand excluded by PLIPPX4.34: 3 residues within 4Å:- Chain D: Y.197
- Ligands: PX4.28, PX4.39
Ligand excluded by PLIPPX4.39: 19 residues within 4Å:- Chain B: I.131, I.138, M.141, F.145, G.168, E.169, F.171, Y.172, F.175, M.213, L.216
- Chain D: M.192, P.196, W.199, F.207
- Ligands: PX4.19, LMT.24, PX4.28, PX4.34
Ligand excluded by PLIPPX4.40: 15 residues within 4Å:- Chain A: L.143, Y.146, T.166, L.167, G.168
- Chain D: I.26, V.27, I.31, G.34, S.38, K.39, T.40, L.113
- Ligands: PX4.27, PX4.46
Ligand excluded by PLIPPX4.41: 13 residues within 4Å:- Chain D: P.79, W.80, F.83, S.125, A.126, L.127, I.128, S.129, I.131, P.132
- Ligands: PX4.43, PX4.44, PX4.45
Ligand excluded by PLIPPX4.42: 7 residues within 4Å:- Chain A: Y.197, W.199, I.203, P.204
- Ligands: LMT.1, PX4.43, PX4.44
Ligand excluded by PLIPPX4.43: 5 residues within 4Å:- Ligands: PX4.3, 1N7.14, PX4.41, PX4.42, PX4.44
Ligand excluded by PLIPPX4.44: 5 residues within 4Å:- Ligands: 1N7.14, PX4.41, PX4.42, PX4.43, PX4.45
Ligand excluded by PLIPPX4.45: 10 residues within 4Å:- Chain D: K.77, P.79, W.80, L.82, F.83, F.86, I.90, S.125
- Ligands: PX4.41, PX4.44
Ligand excluded by PLIPPX4.46: 3 residues within 4Å:- Chain C: Y.197
- Ligands: PX4.27, PX4.40
Ligand excluded by PLIP- 4 x CA: CALCIUM ION(Non-functional Binders)
CA.11: 3 residues within 4Å:- Ligands: CA.23, CA.35, CA.47
No protein-ligand interaction detected (PLIP)CA.23: 3 residues within 4Å:- Ligands: CA.11, CA.35, CA.47
No protein-ligand interaction detected (PLIP)CA.35: 3 residues within 4Å:- Ligands: CA.11, CA.23, CA.47
No protein-ligand interaction detected (PLIP)CA.47: 3 residues within 4Å:- Ligands: CA.11, CA.23, CA.35
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 2.70 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)(Non-functional Binders)
- 4 x CA: CALCIUM ION(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.