SMTL ID : 6a6m.1

Crystal structure of an outward-open nucleotide-bound state of the eukaryotic ABC multidrug transporter CmABCB1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.2 29 PLIP interactions: 20 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: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:D.121, A:S.388, A:K.392, A:S.393, A:Q.397, A:D.517, B:R.218, B:A.522 pi-Stacking: A:Y.360, A:Y.360 ANP.7: 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.8 27 PLIP interactions: 18 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:R.363, B:G.387, B:A.390, B:G.391, B:K.392, B:K.392, B:S.393, 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.388, B:K.392, B:S.393, B:Q.397, B:D.517, A:R.218, A:A.522 pi-Stacking: B:Y.360, B:Y.360

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.8: 3 residues within 4Å: Chain B: S.393, Q.437 Ligands: ANP.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.393, H2O.20, H2O.22

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

DMU.3: 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, Y.588, L.591, Q.595 Chain B: S.473, F.474, D.524 Ligands: NO3.6 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.588, A:L.591, A:L.591, B:D.524 Hydrogen bonds: A:G.387, A:G.389, A:Q.566, B:S.473 Water bridges: A:S.388, A:G.389 DMU.4: 3 residues within 4Å: Chain A: F.18, A.19, W.22 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.15 DMU.5: 5 residues within 4Å: Chain A: G.87, A.91 Chain B: R.245, I.249, L.253 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.249, B:L.253, A:A.91 DMU.9: 18 residues within 4Å: Chain A: S.473, F.474, 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, Y.588, L.591, Q.595 Ligands: NO3.12 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.588, B:L.591, B:L.591, A:D.524 Hydrogen bonds: B:G.387, B:G.389, B:Q.566, A:S.473 Water bridges: B:S.388, B:G.389 DMU.10: 3 residues within 4Å: Chain B: F.18, A.19, W.22 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.15 DMU.11: 5 residues within 4Å: Chain A: R.245, I.249, L.253 Chain B: G.87, A.91 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.249, A:L.253, B:A.91

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

NO3.6: 6 residues within 4Å: Chain A: S.388, G.389 Chain B: F.474, Q.497, R.500 Ligands: DMU.3 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.497, B:R.500, B:R.500 Water bridges: B:F.474, A:G.389 NO3.12: 6 residues within 4Å: Chain A: F.474, Q.497, R.500 Chain B: S.388, G.389 Ligands: DMU.9 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.497, A:R.500, A:R.500 Water bridges: A:F.474, B:G.389

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kodan, A. et al., Inward- and outward-facing X-ray crystal structures of homodimeric P-glycoprotein CmABCB1. Nat Commun (2019)

Release Date

2019-02-20

Peptides

ATP-binding cassette, sub-family B, member 1: 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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ATP-binding cassette, sub-family B, member 1

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