SMTL ID : 7dqv.1

Crystal structure of a CmABCB1 mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 22 residues within 4Å: Chain A: Y.360, T.362, R.363, V.368, G.387, S.388, G.389, A.390, G.391, K.392, S.393, T.394, Y.403, Q.437 Chain B: L.491, A.492, L.493, S.494, G.495, G.496, Q.497 Ligands: MG.5 28 PLIP interactions: 19 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:R.363, A:G.387, A:A.390, A:G.391, A:K.392, A:K.392, A:S.393, A:T.394, A:T.394, A:Y.403, A:Q.437, B:L.491, B:S.494, B:S.494, B:G.495, B:G.496, B:Q.497, B:Q.497 Water bridges: A:S.393, A:S.393, A:S.393, A:D.517, A:E.518, A:H.551, B:R.218, B:A.522 pi-Stacking: A:Y.360, A:Y.360 ANP.6: 22 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, G.389, A.390, G.391, K.392, S.393, T.394, Y.403, Q.437 Ligands: MG.10 28 PLIP interactions: 18 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:T.362, B:R.363, B:G.387, B:A.390, B:G.391, B:K.392, B:K.392, B:S.393, B:T.394, B:Y.403, B:Q.437, A:L.491, 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:D.517, B:H.551, A:R.218, A:A.522, A:A.522 pi-Stacking: B:Y.360, B:Y.360

4 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.2: 18 residues within 4Å: Chain A: G.386, G.387, S.388, G.389, A.390, H.551, R.552, L.553, Q.566, D.567, F.587, L.591, Q.595 Chain B: S.473, F.474, A.477, D.524 Ligands: NO3.4 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.551, A:L.553, B:D.524 Hydrogen bonds: A:G.389, A:Q.566, A:D.567, B:S.473 Water bridges: A:G.387, A:G.387, A:S.388 DMU.3: 7 residues within 4Å: Chain A: F.18, A.19, W.22, I.29, F.33, L.146, L.150 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.18, A:F.18, A:I.29, A:F.33, A:F.33, A:F.33, A:L.146 DMU.7: 18 residues within 4Å: Chain A: S.473, F.474, A.477, D.524 Chain B: G.386, G.387, S.388, G.389, A.390, H.551, R.552, L.553, Q.566, D.567, F.587, L.591, Q.595 Ligands: NO3.9 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:H.551, B:L.553, A:D.524 Hydrogen bonds: B:G.389, B:Q.566, B:D.567, A:S.473 Water bridges: B:G.387, B:G.387, B:S.388 DMU.8: 7 residues within 4Å: Chain B: F.18, A.19, W.22, I.29, F.33, L.146, L.150 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.18, B:F.18, B:I.29, B:F.33, B:F.33, B:F.33, B:L.146

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 6 residues within 4Å: Chain A: S.388, G.389 Chain B: F.474, Q.497, R.500 Ligands: DMU.2 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.389, B:Q.497, B:R.500, B:R.500 Water bridges: B:F.474 NO3.9: 6 residues within 4Å: Chain A: F.474, Q.497, R.500 Chain B: S.388, G.389 Ligands: DMU.7 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.497, A:R.500, A:R.500, B:G.389 Water bridges: A:F.474

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 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.3, H2O.6 MG.10: 3 residues within 4Å: Chain B: S.393, Q.437 Ligands: ANP.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.393, H2O.17, H2O.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsuoka, K. et al., The crystal structure of the CmABCB1 G132V mutant, which favors the outward-facing state, reveals the mechanism of the pivotal joint between TM1 and TM3. Protein Sci. (2021)

Release Date

2021-03-24

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