SMTL ID : 6m60.1

Plumbagin in complex with CRM1#-Ran-RanBP1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.24, T.42 Ligands: GTP.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.42, H2O.1, H2O.1

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: D.125, S.153, Y.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.153 GOL.13: 7 residues within 4Å: Chain C: I.356, E.357, E.358, R.359, F.362, N.400, V.402 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.356, C:E.358, C:N.400 GOL.14: 7 residues within 4Å: Chain C: M.320, T.323, A.327, T.364, D.367, Y.368 Ligands: NO3.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.364

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

NO3.3: 5 residues within 4Å: Chain A: V.137, R.140, K.141 Chain C: M.320 Ligands: GOL.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.140 NO3.4: 4 residues within 4Å: Chain A: L.31, P.49, L.50, V.51 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.31, A:V.51 Water bridges: B:K.72 NO3.6: 6 residues within 4Å: Chain A: H.139, R.140, L.144 Chain C: Q.316, E.360, L.361 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.140 NO3.7: 6 residues within 4Å: Chain A: A.133, I.136, H.139, Y.146 Chain C: E.360, K.363 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.363 NO3.12: 6 residues within 4Å: Chain C: S.882, F.885, F.886, T.889, M.943, F.948 No protein-ligand interaction detected (PLIP) NO3.15: 3 residues within 4Å: Chain C: W.445, S.446, W.447 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.445, C:W.447 Water bridges: C:H.448 NO3.16: 5 residues within 4Å: Chain C: V.586, P.617, N.646, I.647, T.650 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.650 NO3.17: 6 residues within 4Å: Chain C: R.80, K.81, H.950, K.985, E.986, V.987 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.80, C:R.80 Water bridges: C:K.81 NO3.19: 4 residues within 4Å: Chain C: K.894, F.897, R.978, L.981 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.978

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.5: 28 residues within 4Å: Chain A: D.18, G.19, G.20, T.21, G.22, K.23, T.24, T.25, F.35, E.36, K.37, K.38, Y.39, V.40, A.41, T.42, T.66, A.67, G.68, L.69, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.1 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:G.20, A:T.21, A:G.22, A:K.23, A:T.24, A:T.24, A:T.25, A:T.25, A:E.36, A:Y.39, A:T.42, A:T.66, A:G.68, A:N.122, A:K.123, A:K.123, A:A.151, A:K.152 Water bridges: A:T.24, A:V.40, A:T.42, A:T.42, A:L.69, A:L.69 Salt bridges: A:K.23, A:K.23, A:D.125 pi-Stacking: A:F.35, A:F.35

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

CL.8: 2 residues within 4Å: Chain C: K.512, H.554 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain C: A.327, R.328, R.330, A.331 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain C: K.186, S.190 Ligand excluded by PLIP

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.11: 5 residues within 4Å: Chain C: W.51, L.77, K.81, L.84, L.85 No protein-ligand interaction detected (PLIP) DMS.18: 3 residues within 4Å: Chain C: N.791, D.832, W.836 2 PLIP interactions: 2 interactions with chain C pi-Cation interactions: C:W.836, C:W.836 DMS.20: 5 residues within 4Å: Chain C: I.500, F.517, T.520, V.521 Ligands: F2X.23 No protein-ligand interaction detected (PLIP)

3 x F2X: (2~{R})-2-methyl-5-oxidanyl-2,3-dihydronaphthalene-1,4-dione(Covalent)

F2X.21: 7 residues within 4Å: Chain C: I.908, S.909, Y.912, Q.933, T.964, K.965, C.967 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.912, C:Y.912, C:Y.912, C:Q.933 Hydrogen bonds: C:I.908 F2X.22: 8 residues within 4Å: Chain C: S.148, S.149, S.151, V.152, C.155, L.199, V.203, L.212 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.199, C:V.203 F2X.23: 8 residues within 4Å: Chain C: L.481, C.484, E.485, A.497, I.500, K.524, F.528 Ligands: DMS.20 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.481, C:E.485, C:K.524 pi-Cation interactions: C:K.524

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lei, Y. et al., Novel Mechanistic Observations and NES-Binding Groove Features Revealed by the CRM1 Inhibitors Plumbagin and Oridonin. J.Nat.Prod. (2021)

Release Date

2021-06-09

Peptides

GTP-binding nuclear protein Ran: A
Ran-specific GTPase-activating protein 1: B
Exportin-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GTP-binding nuclear protein Ran

Ran-specific GTPase-activating protein 1

Exportin-1

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