SMTL ID : 7jm7.1

Structure of human CLC-7/OSTM1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 11 residues within 4Å: Chain A: H.253, E.259, N.263, K.267 Chain C: M.148, A.149, D.150, R.151, Q.153, V.156, E.160 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.153, C:Q.153 NAG-NAG-BMA-MAN-MAN.4: 11 residues within 4Å: Chain A: M.148, A.149, D.150, R.151, Q.153, V.156, E.160 Chain C: H.253, E.259, N.263, K.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.153, A:Q.153

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.2: 4 residues within 4Å: Chain A: E.181, L.182, S.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: F.193, N.194, L.197 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: E.181, L.182, S.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: F.193, N.194, L.197 No protein-ligand interaction detected (PLIP)

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.7: 2 residues within 4Å: Chain A: N.93, E.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.93 NAG.8: 4 residues within 4Å: Chain A: E.86, L.87, S.124, N.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.128, A:N.128 NAG.9: 1 residues within 4Å: Chain A: N.274 No protein-ligand interaction detected (PLIP) NAG.10: 7 residues within 4Å: Chain A: F.119, Q.120, V.123, M.126, S.159, E.160, N.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.163 NAG.17: 1 residues within 4Å: Chain C: N.93 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.93 NAG.18: 4 residues within 4Å: Chain C: E.86, L.87, S.124, N.128 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.128, C:N.128 NAG.19: 1 residues within 4Å: Chain C: N.274 No protein-ligand interaction detected (PLIP) NAG.20: 7 residues within 4Å: Chain C: F.119, Q.120, V.123, M.126, S.159, E.160, N.163 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.163

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.11: 21 residues within 4Å: Chain B: E.95, S.96, S.632, P.634, V.635, T.636, S.656, N.657, H.658, N.659, G.660, F.661, P.662, R.767, H.768, L.781, T.783, R.784, K.785, D.786 Ligands: MG.12 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.96, B:S.96, B:S.96, B:S.96, B:S.632, B:T.636, B:T.636, B:N.659, B:N.659, B:D.786, B:D.786 Salt bridges: B:H.658, B:R.767, B:R.767, B:H.768, B:K.785, B:K.785 pi-Stacking: B:H.658, B:H.658 ATP.21: 21 residues within 4Å: Chain D: E.95, S.96, S.632, P.634, V.635, T.636, S.656, N.657, H.658, N.659, G.660, F.661, P.662, R.767, H.768, L.781, T.783, R.784, K.785, D.786 Ligands: MG.22 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:E.95, D:S.96, D:S.96, D:S.96, D:S.96, D:S.632, D:T.636, D:T.636, D:N.659, D:N.659, D:T.783, D:D.786 Salt bridges: D:H.658, D:R.767, D:R.767, D:H.768, D:K.785, D:K.785 pi-Stacking: D:H.658, D:H.658

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain B: E.95, N.659 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.95 MG.22: 3 residues within 4Å: Chain D: E.95, N.659 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.95

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 7 residues within 4Å: Chain B: S.204, I.206, G.248, G.512, V.513, F.514, Y.602 Ligand excluded by PLIP CL.14: 7 residues within 4Å: Chain B: G.245, E.247, G.248, G.512, V.513, F.514, I.515 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain B: G.203, S.204, G.205, P.207, Q.208, Y.505 Ligand excluded by PLIP CL.23: 7 residues within 4Å: Chain D: S.204, I.206, G.248, G.512, V.513, F.514, Y.602 Ligand excluded by PLIP CL.24: 7 residues within 4Å: Chain D: G.245, E.247, G.248, G.512, V.513, F.514, I.515 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain D: G.203, S.204, G.205, P.207, Q.208, Y.505 Ligand excluded by PLIP

2 x 0J1: (2R)-3-{[(R)-hydroxy{[(1S,2R,3S,4S,5R,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dinonanoate(Non-covalent)

0J1.16: 26 residues within 4Å: Chain B: L.132, L.136, L.139, V.140, P.219, V.222, R.223, L.224, L.227, V.256, I.257, A.259, G.260, I.261, Q.263, G.264, R.265, S.266, T.267, S.268, F.273, I.275, F.276, K.285, P.716, R.717 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.132, B:L.136, B:L.139, B:V.140, B:L.227, B:I.257, B:I.261, B:I.275 Hydrogen bonds: B:L.224, B:A.259, B:R.265, B:S.266, B:S.266, B:T.267, B:S.268, B:S.268, B:K.285 Salt bridges: B:R.223, B:K.285, B:R.717 0J1.26: 26 residues within 4Å: Chain D: L.132, L.136, L.139, V.140, P.219, V.222, R.223, L.224, L.227, V.256, I.257, A.259, G.260, I.261, Q.263, G.264, R.265, S.266, T.267, S.268, F.273, I.275, F.276, K.285, P.716, R.717 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:L.136, D:L.139, D:V.140, D:L.227, D:I.257, D:I.261 Hydrogen bonds: D:L.224, D:A.259, D:R.265, D:S.266, D:S.266, D:T.267, D:S.268, D:S.268, D:K.285 Salt bridges: D:R.223, D:K.285, D:R.717

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schrecker, M. et al., Cryo-EM structure of the lysosomal chloride-proton exchanger CLC-7 in complex with OSTM1. Elife (2020)

Release Date

2020-09-02

Peptides

Osteopetrosis-associated transmembrane protein 1: AC
H(+)/Cl(-) exchange transporter 7: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
D

B
A

D
C

Membrane

We predict this structure to be a membrane protein.
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Osteopetrosis-associated transmembrane protein 1

H(+)/Cl(-) exchange transporter 7

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