- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CA: CALCIUM ION(Non-functional Binders)
- 8 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.2: 18 residues within 4Å:- Chain A: M.134, M.178, T.179, L.180, T.210, M.213, I.214
- Chain C: L.180, F.207, V.208, T.210, F.211
- Ligands: PX4.7, PX4.10, LMT.12, LMT.22, PX4.25, LMT.32
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain A- Hydrophobic interactions: C:F.207, C:V.208, C:T.210
- Hydrogen bonds: A:M.178
LMT.3: 12 residues within 4Å:- Chain A: F.148, M.151, L.155, R.159, Y.195, Y.197, V.200, F.201
- Chain D: E.100, I.101
- Ligands: PX4.38, PX4.39
7 PLIP interactions:2 interactions with chain D, 5 interactions with chain A- Hydrophobic interactions: D:I.101, A:F.148, A:L.155, A:F.201
- Hydrogen bonds: D:E.100, A:Y.195, A:Y.197
LMT.12: 18 residues within 4Å:- Chain B: M.134, M.178, T.179, L.180, T.210, M.213, I.214
- Chain D: L.180, F.207, V.208, T.210, F.211
- Ligands: LMT.2, PX4.17, PX4.20, LMT.22, LMT.32, PX4.35
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain B- Hydrophobic interactions: D:F.207, D:V.208, D:T.210
- Hydrogen bonds: B:M.178
LMT.13: 12 residues within 4Å:- Chain B: F.148, M.151, L.155, R.159, Y.195, Y.197, V.200, F.201
- Chain C: E.100, I.101
- Ligands: PX4.28, PX4.29
7 PLIP interactions:5 interactions with chain B, 2 interactions with chain C- Hydrophobic interactions: B:F.148, B:L.155, B:F.201, C:I.101
- Hydrogen bonds: B:Y.195, B:Y.197, C:E.100
LMT.22: 18 residues within 4Å:- Chain B: L.180, F.207, V.208, T.210, F.211
- Chain C: M.134, M.178, T.179, L.180, T.210, M.213, I.214
- Ligands: LMT.2, LMT.12, PX4.15, PX4.27, PX4.30, LMT.32
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain C- Hydrophobic interactions: B:F.207, B:V.208, B:T.210
- Hydrogen bonds: C:M.178
LMT.23: 12 residues within 4Å:- Chain A: E.100, I.101
- Chain C: F.148, M.151, L.155, R.159, Y.195, Y.197, V.200, F.201
- Ligands: PX4.8, PX4.9
7 PLIP interactions:5 interactions with chain C, 2 interactions with chain A- Hydrophobic interactions: C:F.148, C:L.155, C:F.201, A:I.101
- Hydrogen bonds: C:Y.195, C:Y.197, A:E.100
LMT.32: 18 residues within 4Å:- Chain A: L.180, F.207, V.208, T.210, F.211
- Chain D: M.134, M.178, T.179, L.180, T.210, M.213, I.214
- Ligands: LMT.2, PX4.5, LMT.12, LMT.22, PX4.37, PX4.40
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain D- Hydrophobic interactions: A:F.207, A:V.208, A:T.210
- Hydrogen bonds: D:M.178
LMT.33: 12 residues within 4Å:- Chain B: E.100, I.101
- Chain D: F.148, M.151, L.155, R.159, Y.195, Y.197, V.200, F.201
- Ligands: PX4.18, PX4.19
7 PLIP interactions:2 interactions with chain B, 5 interactions with chain D- Hydrophobic interactions: B:I.101, D:F.148, D:L.155, D:F.201
- Hydrogen bonds: B:E.100, D:Y.195, D:Y.197
- 4 x 1N7: CHAPSO(Non-covalent)
1N7.4: 7 residues within 4Å:- Chain A: Q.119
- Chain C: P.132, G.133, L.135, S.136, D.223
- Ligands: PX4.30
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:L.135
- Hydrogen bonds: C:S.136, C:S.136
1N7.14: 7 residues within 4Å:- Chain B: Q.119
- Chain D: P.132, G.133, L.135, S.136, D.223
- Ligands: PX4.40
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:L.135
- Hydrogen bonds: D:S.136, D:S.136
1N7.24: 7 residues within 4Å:- Chain B: P.132, G.133, L.135, S.136, D.223
- Chain C: Q.119
- Ligands: PX4.20
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.135
- Hydrogen bonds: B:S.136, B:S.136
1N7.34: 7 residues within 4Å:- Chain A: P.132, G.133, L.135, S.136, D.223
- Chain D: Q.119
- Ligands: PX4.10
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:L.135
- Hydrogen bonds: A:S.136, A:S.136
- 24 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
PX4.5: 21 residues within 4Å:- Chain A: M.192, P.196, Y.197, W.199, F.207
- Chain D: I.131, I.138, M.141, T.142, F.145, T.166, G.168, E.169, F.171, Y.172, F.175, M.213
- Ligands: PX4.16, LMT.32, PX4.39, PX4.40
Ligand excluded by PLIPPX4.6: 16 residues within 4Å:- Chain A: V.27, G.30, I.31, G.34, S.38, K.39, T.40, L.113
- Chain C: T.142, L.143, Y.146, T.166, L.167, G.168, F.171
- Ligands: PX4.15
Ligand excluded by PLIPPX4.7: 14 residues within 4Å:- Chain A: P.79, W.80, F.83, F.111, T.115, S.125, I.128, S.129, I.131, P.132
- Chain C: L.140
- Ligands: LMT.2, PX4.8, PX4.10
Ligand excluded by PLIPPX4.8: 8 residues within 4Å:- Chain A: P.79, W.80, F.83, F.111
- Ligands: PX4.7, PX4.9, PX4.10, LMT.23
Ligand excluded by PLIPPX4.9: 10 residues within 4Å:- Chain A: F.99, I.101
- Chain C: P.196, Y.197, W.199, P.204
- Ligands: PX4.8, PX4.10, LMT.23, PX4.25
Ligand excluded by PLIPPX4.10: 7 residues within 4Å:- Chain A: L.135
- Ligands: LMT.2, PX4.7, PX4.8, PX4.9, PX4.25, 1N7.34
Ligand excluded by PLIPPX4.15: 21 residues within 4Å:- Chain B: M.192, P.196, Y.197, W.199, F.207
- Chain C: I.131, I.138, M.141, T.142, F.145, T.166, G.168, E.169, F.171, Y.172, F.175, M.213
- Ligands: PX4.6, LMT.22, PX4.29, PX4.30
Ligand excluded by PLIPPX4.16: 16 residues within 4Å:- Chain B: V.27, G.30, I.31, G.34, S.38, K.39, T.40, L.113
- Chain D: T.142, L.143, Y.146, T.166, L.167, G.168, F.171
- Ligands: PX4.5
Ligand excluded by PLIPPX4.17: 14 residues within 4Å:- Chain B: P.79, W.80, F.83, F.111, T.115, S.125, I.128, S.129, I.131, P.132
- Chain D: L.140
- Ligands: LMT.12, PX4.18, PX4.20
Ligand excluded by PLIPPX4.18: 8 residues within 4Å:- Chain B: P.79, W.80, F.83, F.111
- Ligands: PX4.17, PX4.19, PX4.20, LMT.33
Ligand excluded by PLIPPX4.19: 10 residues within 4Å:- Chain B: F.99, I.101
- Chain D: P.196, Y.197, W.199, P.204
- Ligands: PX4.18, PX4.20, LMT.33, PX4.35
Ligand excluded by PLIPPX4.20: 7 residues within 4Å:- Chain B: L.135
- Ligands: LMT.12, PX4.17, PX4.18, PX4.19, 1N7.24, PX4.35
Ligand excluded by PLIPPX4.25: 21 residues within 4Å:- Chain A: I.131, I.138, M.141, T.142, F.145, T.166, G.168, E.169, F.171, Y.172, F.175, M.213
- Chain C: M.192, P.196, Y.197, W.199, F.207
- Ligands: LMT.2, PX4.9, PX4.10, PX4.36
Ligand excluded by PLIPPX4.26: 16 residues within 4Å:- Chain B: T.142, L.143, Y.146, T.166, L.167, G.168, F.171
- Chain C: V.27, G.30, I.31, G.34, S.38, K.39, T.40, L.113
- Ligands: PX4.35
Ligand excluded by PLIPPX4.27: 14 residues within 4Å:- Chain B: L.140
- Chain C: P.79, W.80, F.83, F.111, T.115, S.125, I.128, S.129, I.131, P.132
- Ligands: LMT.22, PX4.28, PX4.30
Ligand excluded by PLIPPX4.28: 8 residues within 4Å:- Chain C: P.79, W.80, F.83, F.111
- Ligands: LMT.13, PX4.27, PX4.29, PX4.30
Ligand excluded by PLIPPX4.29: 10 residues within 4Å:- Chain B: P.196, Y.197, W.199, P.204
- Chain C: F.99, I.101
- Ligands: LMT.13, PX4.15, PX4.28, PX4.30
Ligand excluded by PLIPPX4.30: 7 residues within 4Å:- Chain C: L.135
- Ligands: 1N7.4, PX4.15, LMT.22, PX4.27, PX4.28, PX4.29
Ligand excluded by PLIPPX4.35: 21 residues within 4Å:- Chain B: I.131, I.138, M.141, T.142, F.145, T.166, G.168, E.169, F.171, Y.172, F.175, M.213
- Chain D: M.192, P.196, Y.197, W.199, F.207
- Ligands: LMT.12, PX4.19, PX4.20, PX4.26
Ligand excluded by PLIPPX4.36: 16 residues within 4Å:- Chain A: T.142, L.143, Y.146, T.166, L.167, G.168, F.171
- Chain D: V.27, G.30, I.31, G.34, S.38, K.39, T.40, L.113
- Ligands: PX4.25
Ligand excluded by PLIPPX4.37: 14 residues within 4Å:- Chain A: L.140
- Chain D: P.79, W.80, F.83, F.111, T.115, S.125, I.128, S.129, I.131, P.132
- Ligands: LMT.32, PX4.38, PX4.40
Ligand excluded by PLIPPX4.38: 8 residues within 4Å:- Chain D: P.79, W.80, F.83, F.111
- Ligands: LMT.3, PX4.37, PX4.39, PX4.40
Ligand excluded by PLIPPX4.39: 10 residues within 4Å:- Chain A: P.196, Y.197, W.199, P.204
- Chain D: F.99, I.101
- Ligands: LMT.3, PX4.5, PX4.38, PX4.40
Ligand excluded by PLIPPX4.40: 7 residues within 4Å:- Chain D: L.135
- Ligands: PX4.5, 1N7.14, LMT.32, PX4.37, PX4.38, PX4.39
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Irie, K. et al., Structural insight on the voltage dependence of prokaryotic voltage gated sodium channel NavAb. FEBS Lett. (2017)
- Release Date
- 2017-12-27
- 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 2.80 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CA: CALCIUM ION(Non-functional Binders)
- 8 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
- 4 x 1N7: CHAPSO(Non-covalent)
- 24 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Irie, K. et al., Structural insight on the voltage dependence of prokaryotic voltage gated sodium channel NavAb. FEBS Lett. (2017)
- Release Date
- 2017-12-27
- 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.