SMTL ID : 4wmu.1

STRUCTURE OF MBP-MCL1 BOUND TO ligand 2 AT 1.55A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 16 residues within 4Å: Chain A: N.13, D.15, K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, M.331, W.341, R.345 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.63, A:R.67, A:R.67, A:E.154, A:Y.156, A:R.345

1 x 19H: 6-chloro-3-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1H-indole-2-carboxylic acid(Non-covalent)

19H.2: 15 residues within 4Å: Chain A: A.424, F.425, M.428, L.432, L.443, V.446, M.447, V.450, F.451, R.460, T.463, L.464, F.467, G.468, I.491 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.425, A:L.432, A:V.446, A:V.450, A:F.451, A:T.463, A:F.467, A:F.467, A:F.467, A:I.491 Hydrogen bonds: A:V.450 Salt bridges: A:R.460 pi-Stacking: A:F.467 Halogen bonds: A:A.424

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.364 Ligands: FMT.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.364, H2O.1, H2O.3, H2O.3 MG.4: 1 residues within 4Å: Chain A: S.399 No protein-ligand interaction detected (PLIP)

13 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 5 residues within 4Å: Chain A: R.497, T.498, K.499, R.500, D.501 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.501, A:D.501 FMT.6: 6 residues within 4Å: Chain A: K.363, D.364, T.367, V.504, R.507 Ligands: MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.363, A:T.367 Water bridges: A:D.364, A:D.364, A:D.364, A:V.504 FMT.7: 3 residues within 4Å: Chain A: T.346, N.350, R.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.350 Water bridges: A:N.350, A:R.355 FMT.8: 2 residues within 4Å: Chain A: D.392, A.394 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.393, A:T.393, A:A.394 FMT.9: 4 residues within 4Å: Chain A: A.72, L.77, E.79, I.105 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.79 FMT.10: 6 residues within 4Å: Chain A: N.219, K.220, G.221, S.239, V.241 Ligands: FMT.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.239 FMT.11: 4 residues within 4Å: Chain A: G.244, V.245, R.317 Ligands: FMT.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.245 FMT.12: 3 residues within 4Å: Chain A: Y.243, R.317 Ligands: FMT.11 No protein-ligand interaction detected (PLIP) FMT.13: 4 residues within 4Å: Chain A: N.119, L.122, G.221 Ligands: FMT.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.119 FMT.14: 3 residues within 4Å: Chain A: T.32, L.276, E.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.279 FMT.15: 4 residues within 4Å: Chain A: V.245, T.246, V.247, E.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.245, A:V.247 FMT.16: 3 residues within 4Å: Chain A: N.151, E.154, Y.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.151 FMT.17: 2 residues within 4Å: Chain A: N.125, P.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125

1 x NA: SODIUM ION(Non-functional Binders)

NA.18: 1 residues within 4Å: Chain A: P.124 No protein-ligand interaction detected (PLIP)

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.19: 6 residues within 4Å: Chain A: H.65, D.96, A.97, I.330, M.331, N.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.65 Water bridges: A:N.333 EDO.20: 4 residues within 4Å: Chain A: M.322, A.325, G.328, I.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.328 Water bridges: A:I.330 EDO.21: 4 residues within 4Å: Chain A: Q.336, A.339, Y.372, D.493 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.493, A:D.493 Water bridges: A:A.339, A:Y.372 EDO.22: 7 residues within 4Å: Chain A: Y.91, F.93, V.111, A.302, V.303, E.309, M.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clifton, M.C. et al., A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1. Plos One (2015)

Release Date

2015-05-06

Peptides

MBP-MCL1 chimera protein,Induced myeloid leukemia cell differentiation protein Mcl-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

MBP-MCL1 chimera protein,Induced myeloid leukemia cell differentiation protein Mcl-1

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