SMTL ID : 4k1c.3 (2 other biounits)

VCX1 Calcium/Proton Exchanger

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

OLC.1: 3 residues within 4Å: Chain A: I.57, F.61, L.63 Ligand excluded by PLIP OLC.2: 8 residues within 4Å: Chain A: Y.152, W.383, V.387, L.390, A.391 Chain B: V.211, L.218, S.226 Ligand excluded by PLIP OLC.3: 7 residues within 4Å: Chain A: E.203, R.206, G.207, W.347 Chain C: A.397, M.398, F.401 Ligand excluded by PLIP OLC.4: 5 residues within 4Å: Chain A: L.56, I.57, H.60, F.61, Q.62 Ligand excluded by PLIP OLC.5: 12 residues within 4Å: Chain A: S.137, L.141, L.145, F.149, I.301, A.305, H.308, V.309, V.312, L.313, M.316, K.317 Ligand excluded by PLIP OLC.22: 3 residues within 4Å: Chain B: I.57, F.61, L.63 Ligand excluded by PLIP OLC.23: 8 residues within 4Å: Chain B: Y.152, W.383, V.387, L.390, A.391 Chain C: V.211, L.218, S.226 Ligand excluded by PLIP OLC.24: 7 residues within 4Å: Chain A: A.397, M.398, F.401 Chain B: E.203, R.206, G.207, W.347 Ligand excluded by PLIP OLC.25: 5 residues within 4Å: Chain B: L.56, I.57, H.60, F.61, Q.62 Ligand excluded by PLIP OLC.26: 12 residues within 4Å: Chain B: S.137, L.141, L.145, F.149, I.301, A.305, H.308, V.309, V.312, L.313, M.316, K.317 Ligand excluded by PLIP OLC.43: 3 residues within 4Å: Chain C: I.57, F.61, L.63 Ligand excluded by PLIP OLC.44: 8 residues within 4Å: Chain A: V.211, L.218, S.226 Chain C: Y.152, W.383, V.387, L.390, A.391 Ligand excluded by PLIP OLC.45: 7 residues within 4Å: Chain B: A.397, M.398, F.401 Chain C: E.203, R.206, G.207, W.347 Ligand excluded by PLIP OLC.46: 5 residues within 4Å: Chain C: L.56, I.57, H.60, F.61, Q.62 Ligand excluded by PLIP OLC.47: 12 residues within 4Å: Chain C: S.137, L.141, L.145, F.149, I.301, A.305, H.308, V.309, V.312, L.313, M.316, K.317 Ligand excluded by PLIP OLC.64: 6 residues within 4Å: Chain D: T.97, L.101, L.220, Y.221, L.224, G.225 Ligand excluded by PLIP OLC.72: 6 residues within 4Å: Chain E: T.97, L.101, L.220, Y.221, L.224, G.225 Ligand excluded by PLIP OLC.80: 6 residues within 4Å: Chain F: T.97, L.101, L.220, Y.221, L.224, G.225 Ligand excluded by PLIP

27 x CA: CALCIUM ION(Non-covalent)

CA.6: 2 residues within 4Å: Chain A: E.307, S.330 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.307, A:E.307, A:S.330, H2O.1, H2O.1 CA.7: 3 residues within 4Å: Chain A: D.378, E.380 Chain B: Q.161 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.378, A:E.380, A:E.380, H2O.1 CA.8: 3 residues within 4Å: Chain A: Q.233, E.236 Chain F: N.153 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.236 CA.9: 3 residues within 4Å: Chain A: E.88, E.235, D.239 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.88, A:E.235, A:E.235, A:D.239, H2O.1 CA.10: 4 residues within 4Å: Chain A: E.88, D.92, E.235, D.239 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.88, A:E.235, A:D.239 CA.27: 2 residues within 4Å: Chain B: E.307, S.330 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.307, B:E.307, B:S.330, H2O.2, H2O.3 CA.28: 3 residues within 4Å: Chain B: D.378, E.380 Chain C: Q.161 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.378, B:E.380, B:E.380, H2O.2 CA.29: 3 residues within 4Å: Chain B: Q.233, E.236 Chain D: N.153 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.236 CA.30: 3 residues within 4Å: Chain B: E.88, E.235, D.239 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.88, B:E.235, B:E.235, B:D.239, H2O.2 CA.31: 4 residues within 4Å: Chain B: E.88, D.92, E.235, D.239 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.88, B:E.235, B:D.239 CA.48: 2 residues within 4Å: Chain C: E.307, S.330 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.307, C:E.307, C:S.330, H2O.4, H2O.4 CA.49: 3 residues within 4Å: Chain A: Q.161 Chain C: D.378, E.380 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.378, C:E.380, C:E.380, H2O.3 CA.50: 3 residues within 4Å: Chain C: Q.233, E.236 Chain E: N.153 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.236 CA.51: 3 residues within 4Å: Chain C: E.88, E.235, D.239 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.88, C:E.235, C:E.235, C:D.239, H2O.3 CA.52: 4 residues within 4Å: Chain C: E.88, D.92, E.235, D.239 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.88, C:E.235, C:D.239 CA.65: 3 residues within 4Å: Chain D: D.378, E.380 Chain F: Q.161 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.378, D:E.380, D:E.380, H2O.4 CA.66: 2 residues within 4Å: Chain D: E.307, S.330 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.307, D:E.307, D:S.330, H2O.5, H2O.5 CA.67: 3 residues within 4Å: Chain D: E.88, E.235, D.239 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.88, D:E.88, D:E.235, D:D.239 CA.68: 3 residues within 4Å: Chain D: E.88, E.235, D.239 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.88, D:E.235, D:E.235, D:D.239 CA.73: 3 residues within 4Å: Chain D: Q.161 Chain E: D.378, E.380 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.378, E:E.380, E:E.380, H2O.6 CA.74: 2 residues within 4Å: Chain E: E.307, S.330 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.307, E:E.307, E:S.330, H2O.6, H2O.6 CA.75: 3 residues within 4Å: Chain E: E.88, E.235, D.239 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.88, E:E.88, E:E.235, E:D.239 CA.76: 3 residues within 4Å: Chain E: E.88, E.235, D.239 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.88, E:E.235, E:E.235, E:D.239 CA.81: 3 residues within 4Å: Chain E: Q.161 Chain F: D.378, E.380 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.378, F:E.380, F:E.380, H2O.7 CA.82: 2 residues within 4Å: Chain F: E.307, S.330 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.307, F:E.307, F:S.330, H2O.7, H2O.7 CA.83: 3 residues within 4Å: Chain F: E.88, E.235, D.239 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.88, F:E.88, F:E.235, F:D.239 CA.84: 3 residues within 4Å: Chain F: E.88, E.235, D.239 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.88, F:E.235, F:E.235, F:D.239

9 x MN: MANGANESE (II) ION(Non-covalent)

MN.11: 5 residues within 4Å: Chain A: D.378, E.380, S.381, E.385 Chain B: S.169 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.378, A:E.380, A:E.385, H2O.1, H2O.2 MN.21: 5 residues within 4Å: Chain A: K.317 Chain F: K.317, K.319 Ligands: IOD.19, IOD.20 No protein-ligand interaction detected (PLIP) MN.32: 5 residues within 4Å: Chain B: D.378, E.380, S.381, E.385 Chain C: S.169 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.378, B:E.380, B:E.385, H2O.2, H2O.3 MN.42: 5 residues within 4Å: Chain B: K.317 Chain D: K.317, K.319 Ligands: IOD.40, IOD.41 No protein-ligand interaction detected (PLIP) MN.53: 5 residues within 4Å: Chain A: S.169 Chain C: D.378, E.380, S.381, E.385 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.378, C:E.380, C:E.385, H2O.4, H2O.4 MN.63: 5 residues within 4Å: Chain C: K.317 Chain E: K.317, K.319 Ligands: IOD.61, IOD.62 No protein-ligand interaction detected (PLIP) MN.69: 4 residues within 4Å: Chain D: D.378, E.380, E.385 Chain F: S.169 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.378, D:E.380, D:E.385, H2O.5, H2O.5 MN.77: 4 residues within 4Å: Chain D: S.169 Chain E: D.378, E.380, E.385 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.378, E:E.380, E:E.385, H2O.6, H2O.6 MN.85: 4 residues within 4Å: Chain E: S.169 Chain F: D.378, E.380, E.385 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.378, F:E.380, F:E.385, H2O.7, H2O.7

33 x IOD: IODIDE ION(Non-functional Binders)

IOD.12: 3 residues within 4Å: Chain A: G.122, V.124, R.125 Ligand excluded by PLIP IOD.13: 4 residues within 4Å: Chain A: R.206, D.350, V.351, P.352 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: Q.62, H.65, T.68 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: H.227, L.230 Ligand excluded by PLIP IOD.16: 7 residues within 4Å: Chain A: L.178, L.179, I.180, P.181, A.182, L.355, F.357 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: N.96, H.228 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: D.35, H.251 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: K.319 Chain F: K.317 Ligands: MN.21 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain A: K.317 Chain F: V.241, T.244 Ligands: MN.21 Ligand excluded by PLIP IOD.33: 3 residues within 4Å: Chain B: G.122, V.124, R.125 Ligand excluded by PLIP IOD.34: 4 residues within 4Å: Chain B: R.206, D.350, V.351, P.352 Ligand excluded by PLIP IOD.35: 3 residues within 4Å: Chain B: Q.62, H.65, T.68 Ligand excluded by PLIP IOD.36: 2 residues within 4Å: Chain B: H.227, L.230 Ligand excluded by PLIP IOD.37: 7 residues within 4Å: Chain B: L.178, L.179, I.180, P.181, A.182, L.355, F.357 Ligand excluded by PLIP IOD.38: 2 residues within 4Å: Chain B: N.96, H.228 Ligand excluded by PLIP IOD.39: 2 residues within 4Å: Chain B: D.35, H.251 Ligand excluded by PLIP IOD.40: 3 residues within 4Å: Chain B: K.319 Chain D: K.317 Ligands: MN.42 Ligand excluded by PLIP IOD.41: 4 residues within 4Å: Chain B: K.317 Chain D: V.241, T.244 Ligands: MN.42 Ligand excluded by PLIP IOD.54: 3 residues within 4Å: Chain C: G.122, V.124, R.125 Ligand excluded by PLIP IOD.55: 4 residues within 4Å: Chain C: R.206, D.350, V.351, P.352 Ligand excluded by PLIP IOD.56: 3 residues within 4Å: Chain C: Q.62, H.65, T.68 Ligand excluded by PLIP IOD.57: 2 residues within 4Å: Chain C: H.227, L.230 Ligand excluded by PLIP IOD.58: 7 residues within 4Å: Chain C: L.178, L.179, I.180, P.181, A.182, L.355, F.357 Ligand excluded by PLIP IOD.59: 2 residues within 4Å: Chain C: N.96, H.228 Ligand excluded by PLIP IOD.60: 2 residues within 4Å: Chain C: D.35, H.251 Ligand excluded by PLIP IOD.61: 3 residues within 4Å: Chain C: K.319 Chain E: K.317 Ligands: MN.63 Ligand excluded by PLIP IOD.62: 4 residues within 4Å: Chain C: K.317 Chain E: V.241, T.244 Ligands: MN.63 Ligand excluded by PLIP IOD.70: 3 residues within 4Å: Chain D: V.155, Q.156 Chain F: H.227 Ligand excluded by PLIP IOD.71: 2 residues within 4Å: Chain D: H.227, L.230 Ligand excluded by PLIP IOD.78: 3 residues within 4Å: Chain D: H.227 Chain E: V.155, Q.156 Ligand excluded by PLIP IOD.79: 2 residues within 4Å: Chain E: H.227, L.230 Ligand excluded by PLIP IOD.86: 3 residues within 4Å: Chain E: H.227 Chain F: V.155, Q.156 Ligand excluded by PLIP IOD.87: 2 residues within 4Å: Chain F: H.227, L.230 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Waight, A.B. et al., Structural basis for alternating access of a eukaryotic calcium/proton exchanger. Nature (2013)

Release Date

2013-05-08

Peptides

Vacuolar calcium ion transporter: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
B

E
B

F
B

Membrane

We predict this structure to be a membrane protein.
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Vacuolar calcium ion transporter

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