SMTL ID : 3v5u.1

Structure of Sodium/Calcium Exchanger from Methanocaldococcus jannaschii DSM 2661

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

3 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: A.47, T.50, S.51, E.213, S.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.51 NA.3: 5 residues within 4Å: Chain A: E.54, S.77, A.206, T.209, S.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.209, A:T.209 NA.4: 8 residues within 4Å: Chain A: S.51, E.54, N.81, S.210, E.213, S.236, D.240 Ligands: CA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.81, A:E.213

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: T.50, S.51, E.54, T.209, S.210, E.213 Ligands: NA.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.50, A:E.54, A:E.54, A:T.209, A:E.213 CA.5: 5 residues within 4Å: Chain A: I.118, D.121, G.122, D.127 Ligands: OLC.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.118, A:D.121, A:G.122, A:D.127, H2O.2

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: I.14, Y.17, Y.18 Ligands: OLC.24 No protein-ligand interaction detected (PLIP) ACT.7: 1 residues within 4Å: Chain A: Y.60 No protein-ligand interaction detected (PLIP) ACT.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.9: 3 residues within 4Å: Chain A: K.279, R.282, W.283 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.282, A:R.282, A:W.283, A:Q.284 Salt bridges: A:K.279

5 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.10: 9 residues within 4Å: Chain A: L.110, I.113, F.114, V.117, I.118, D.121, D.127 Ligands: CA.5, OLC.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.113, A:F.114, A:F.114, A:F.114, A:I.118 Hydrogen bonds: A:D.127 Water bridges: A:D.121, A:S.124 OLC.11: 10 residues within 4Å: Chain A: V.107, F.111, F.114, I.118, I.126, D.127, V.130, L.134, Y.138 Ligands: OLC.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.107, A:F.114, A:F.114, A:F.114, A:V.130, A:L.134, A:Y.138 Water bridges: A:D.127 OLC.12: 10 residues within 4Å: Chain A: F.182, K.187, A.190, I.195, S.196, D.197, K.198, G.201, L.204, V.205 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.182, A:K.187, A:V.205 Hydrogen bonds: A:D.197 OLC.23: 9 residues within 4Å: Chain A: L.52, P.53, L.56, L.172, L.176, A.179, E.180, G.208, T.209 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.172, A:L.176 Hydrogen bonds: A:E.180, A:G.208 OLC.24: 13 residues within 4Å: Chain A: Y.17, C.80, L.84, L.88, T.203, L.204, A.206, F.207, L.214, Y.292, I.296 Ligands: ACT.6, 1PE.16 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.17, A:L.84, A:L.88, A:L.204, A:F.207, A:L.214 Hydrogen bonds: A:A.206, A:F.207 Water bridges: A:T.203, A:V.205

9 x MYS: PENTADECANE(Non-covalent)(Non-functional Binders)

MYS.13: 3 residues within 4Å: Chain A: A.116, N.258, A.262 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.116 MYS.14: 4 residues within 4Å: Chain A: T.44, I.48, V.143 Ligands: MYS.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.48, A:I.48, A:V.143, A:V.143 MYS.15: 4 residues within 4Å: Chain A: W.283, Q.284, I.286, L.287 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.283, A:L.287 MYS.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MYS.18: 5 residues within 4Å: Chain A: I.136, L.139, R.140, V.247 Ligands: MYS.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.136, A:L.139, A:R.140, A:V.247 MYS.19: 4 residues within 4Å: Chain A: I.91, R.282, I.286, I.293 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.286, A:I.293 MYS.20: 7 residues within 4Å: Chain A: V.259, L.291, I.294, S.298, L.299, R.300 Ligands: MYS.22 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.259, A:V.259, A:L.291, A:I.294, A:R.300 MYS.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MYS.22: 4 residues within 4Å: Chain A: I.293, A.297, S.298 Ligands: MYS.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.293, A:A.297

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.16: 8 residues within 4Å: Chain A: Y.17, S.20, D.21, M.215, L.218, A.219, K.222 Ligands: OLC.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.20, A:K.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liao, J. et al., Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger. Science (2012)

Release Date

2012-02-22

Peptides

Uncharacterized membrane protein MJ0091: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Uncharacterized membrane protein MJ0091

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