SMTL ID : 8py4.1

ABCG2 in complex with ko143 and 5D3 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

NAG-NAG.1: 4 residues within 4Å: Chain C: T.30, S.31, F.54 Chain D: N.606 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: T.30, S.31, F.54 Chain E: N.606 No protein-ligand interaction detected (PLIP)

10 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 6 residues within 4Å: Chain D: Y.580, F.581, Y.586, A.642, C.645, I.649 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.581, D:F.581, D:A.642, D:I.649 CLR.4: 10 residues within 4Å: Chain D: M.533, A.536, I.537, M.558, F.561, L.578, F.581, S.582, F.650, K.657 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.537, D:F.561, D:F.581, D:F.650 CLR.5: 5 residues within 4Å: Chain D: L.481, V.648, L.651, T.652, Y.655 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.648, D:L.651, D:Y.655 CLR.6: 7 residues within 4Å: Chain D: R.388, S.391, K.392, F.395, L.485, P.490, M.493 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.395, D:F.395, D:L.485, D:P.490 CLR.7: 5 residues within 4Å: Chain D: M.493, D.514, F.517, V.518, F.521 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:D.514, D:V.518, D:F.521 CLR.8: 6 residues within 4Å: Chain E: Y.580, F.581, Y.586, A.642, C.645, I.649 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.581, E:F.581, E:A.642, E:I.649 CLR.9: 10 residues within 4Å: Chain E: M.533, A.536, I.537, M.558, F.561, L.578, F.581, S.582, F.650, K.657 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.537, E:F.561, E:F.581, E:F.650 CLR.10: 5 residues within 4Å: Chain E: L.481, V.648, L.651, T.652, Y.655 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.648, E:L.651, E:Y.655 CLR.11: 7 residues within 4Å: Chain E: R.388, S.391, K.392, F.395, L.485, P.490, M.493 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.395, E:F.395, E:L.485, E:P.490 CLR.12: 5 residues within 4Å: Chain E: M.493, D.514, F.517, V.518, F.521 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:D.514, E:V.518, E:F.521

2 x I3O: tert-butyl 3-[(2S,5S,8S)-14-methoxy-2-(2-methylpropyl)-4,7-bis(oxidanylidene)-3,6,17-triazatetracyclo[8.7.0.0^{3,8}.0^{11,16}]heptadeca-1(10),11,13,15-tetraen-5-yl]propanoate(Non-covalent)

I3O.13: 11 residues within 4Å: Chain D: L.549, T.552, V.556, M.559 Chain E: A.407, V.411, L.415, T.445, N.446, S.450 Ligands: I3O.14 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:A.407, E:V.411, E:L.415, D:T.552, D:V.556 Hydrogen bonds: E:N.446 pi-Stacking: E:F.449 I3O.14: 13 residues within 4Å: Chain D: A.407, V.411, L.415, T.445, N.446, F.449, S.450 Chain E: L.549, T.552, I.553, V.556, M.559 Ligands: I3O.13 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:A.407, D:V.411, D:L.415, D:F.449, E:T.552, E:I.553, E:V.556 Hydrogen bonds: D:N.446 pi-Stacking: D:F.449

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Q. et al., Modulation of ABCG2 Transporter Activity by Ko143 Derivatives. Acs Chem.Biol. (2024)

Release Date

2024-11-06

Peptides

5d3(fab) heavy chain variable domain: AC
5D3(Fab) light chain variable domain: BF
Broad substrate specificity ATP-binding cassette transporter ABCG2: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
F

B
E

F
C

D
B

E
A

Membrane

We predict this structure to be a membrane protein.
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5d3(fab) heavy chain variable domain

5D3(Fab) light chain variable domain

Broad substrate specificity ATP-binding cassette transporter ABCG2

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