SMTL ID : 7fc9.1

Crystal structure of CmABCB1 in lipidic mesophase revealed by LCP-SFX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 24 residues within 4Å: Chain A: Y.360, T.362, R.363, V.368, G.387, S.388, A.390, G.391, K.392, S.393, T.394, Y.403, Q.437, E.518, H.551 Chain B: L.491, A.492, L.493, S.494, G.495, G.496, Q.497 Ligands: ZN.2, MG.3 29 PLIP interactions: 22 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:T.362, A:T.362, A:R.363, A:A.390, A:G.391, A:K.392, A:K.392, A:K.392, A:S.393, A:T.394, A:T.394, A:Y.403, A:Q.437, B:S.494, B:S.494, B:G.495, B:G.496, B:Q.497, B:Q.497 Water bridges: A:D.121, A:S.393, A:S.393, A:S.393, A:Q.397, A:Q.397, A:D.517, B:R.218 pi-Stacking: A:Y.360, A:Y.360 ANP.16: 24 residues within 4Å: Chain A: L.491, A.492, L.493, S.494, G.495, G.496, Q.497 Chain B: Y.360, T.362, R.363, V.368, G.387, S.388, A.390, G.391, K.392, S.393, T.394, Y.403, Q.437, E.518, H.551 Ligands: ZN.17, MG.18 27 PLIP interactions: 19 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:T.362, B:T.362, B:R.363, B:A.390, B:G.391, B:K.392, B:K.392, B:K.392, B:S.393, B:T.394, B:Q.437, A:S.494, A:S.494, A:G.495, A:G.496, A:Q.497, A:Q.497 Water bridges: B:S.393, B:S.393, B:S.393, B:Q.397, B:Q.397, B:D.517, A:R.218, A:R.218 pi-Stacking: B:Y.360, B:Y.360

18 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 5 residues within 4Å: Chain A: Q.437, E.518, H.551 Chain B: A.522 Ligands: ANP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.518, A:E.518, A:H.551, H2O.6 ZN.4: 3 residues within 4Å: Chain A: D.135, S.200 Ligands: MG.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.135, A:S.200, H2O.6, H2O.6 ZN.6: 3 residues within 4Å: Chain A: D.459 Ligands: ZN.7, ZN.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.459, H2O.1 ZN.7: 4 residues within 4Å: Chain A: D.459, E.460 Ligands: ZN.6, ZN.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.459, A:E.460, A:E.460 ZN.8: 2 residues within 4Å: Ligands: ZN.6, ZN.7 No protein-ligand interaction detected (PLIP) ZN.9: 2 residues within 4Å: Chain A: H.357, E.367 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.357, A:E.367, A:E.367, H2O.6, H2O.6 ZN.10: 3 residues within 4Å: Chain A: N.355, H.357, G.371 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.357 ZN.11: 2 residues within 4Å: Chain A: E.127, E.201 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.127, A:E.201, A:E.201, H2O.4, H2O.6 ZN.12: 2 residues within 4Å: Chain A: E.39, E.82 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.39, A:E.82, A:E.82, H2O.4, H2O.5 ZN.17: 5 residues within 4Å: Chain A: A.522 Chain B: Q.437, E.518, H.551 Ligands: ANP.16 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.518, B:E.518, B:H.551, H2O.1 ZN.19: 3 residues within 4Å: Chain B: D.135, S.200 Ligands: MG.20 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.135, B:S.200, H2O.11, H2O.12 ZN.21: 3 residues within 4Å: Chain B: D.459 Ligands: ZN.22, ZN.23 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.459, H2O.7 ZN.22: 4 residues within 4Å: Chain B: D.459, E.460 Ligands: ZN.21, ZN.23 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.459, B:E.460, B:E.460 ZN.23: 2 residues within 4Å: Ligands: ZN.21, ZN.22 No protein-ligand interaction detected (PLIP) ZN.24: 2 residues within 4Å: Chain B: H.357, E.367 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.357, B:E.367, B:E.367, H2O.11, H2O.12 ZN.25: 3 residues within 4Å: Chain B: N.355, H.357, G.371 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.357 ZN.26: 2 residues within 4Å: Chain B: E.127, E.201 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.127, B:E.201, B:E.201, H2O.10, H2O.11 ZN.27: 2 residues within 4Å: Chain B: E.39, E.82 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.39, B:E.82, B:E.82, H2O.10, H2O.11

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.393, Q.437 Ligands: ANP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.393, H2O.1, H2O.2 MG.5: 5 residues within 4Å: Chain A: D.135, T.196, S.200, E.320 Ligands: ZN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.135, A:T.196, A:S.200, A:E.320, H2O.6 MG.18: 3 residues within 4Å: Chain B: S.393, Q.437 Ligands: ANP.16 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.393, H2O.7, H2O.8 MG.20: 5 residues within 4Å: Chain B: D.135, T.196, S.200, E.320 Ligands: ZN.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.135, B:T.196, B:S.200, B:E.320, H2O.11

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

CL.13: 1 residues within 4Å: Chain A: H.426 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: H.576 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: H.426 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain B: H.576 Ligand excluded by PLIP

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

ACT.15: 4 residues within 4Å: Chain A: R.401, F.425, R.429 Chain B: K.221 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.425 Hydrogen bonds: A:R.401 Salt bridges: A:R.429, B:K.221 ACT.30: 4 residues within 4Å: Chain A: K.221 Chain B: R.401, F.425, R.429 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.425 Hydrogen bonds: B:R.401 Salt bridges: B:R.429, A:K.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, D. et al., Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX. Iucrj (2022)

Release Date

2022-02-02

Peptides

Probable ATP-dependent transporter ycf16: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Probable ATP-dependent transporter ycf16