SMTL ID : 6m6x.1

Oridonin in complex with CRM1#-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.24, T.42, D.65 Ligands: GTP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.24, A:T.42

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

EDO.2: 4 residues within 4Å: Chain A: N.100, N.103, W.104, D.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.100, A:R.106, A:D.107

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

GTP.3: 27 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, 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 23 PLIP interactions: 23 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 Salt bridges: A:K.23, A:K.23, A:D.125 pi-Stacking: A:F.35, A:F.35

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

CL.4: 3 residues within 4Å: Chain C: T.952, S.953, E.954 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain C: K.512, K.550, K.552, Y.553 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain C: P.64, Q.65, N.116 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain C: R.230 Ligand excluded by PLIP

3 x ODN: (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one(Covalent)

ODN.8: 6 residues within 4Å: Chain C: L.481, C.484, A.497, I.500, K.524, F.528 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.481, C:K.524 ODN.9: 5 residues within 4Å: Chain C: Y.912, D.913, T.964, C.967, K.968 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.912, C:K.968 Hydrogen bonds: C:Y.912 ODN.10: 8 residues within 4Å: Chain C: S.148, S.149, V.152, C.155, V.203, Q.206, G.207, L.212 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.203, C:Q.206, C:L.212

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

2021-03-17

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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