SMTL ID : 6a3c.1

MVM NES mutant Nm12 in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

GTP.1: 26 residues within 4Å: Chain A: D.37, G.38, G.39, T.40, G.41, K.42, T.43, T.44, F.54, E.55, K.56, K.57, Y.58, A.60, T.61, T.85, A.86, G.87, N.141, K.142, D.144, I.145, S.169, A.170, K.171 Ligands: MG.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:G.39, A:T.40, A:T.40, A:G.41, A:K.42, A:T.43, A:T.43, A:T.44, A:T.44, A:E.55, A:T.61, A:T.61, A:T.85, A:G.87, A:N.141, A:K.142, A:K.142, A:A.170, A:K.171 Water bridges: A:V.59, A:Q.88, A:Q.88 Salt bridges: A:K.42, A:K.42, A:D.144 pi-Stacking: A:F.54, A:F.54

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.43, T.61, D.84 Ligands: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.43, A:T.61, H2O.1, H2O.1

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

EDO.3: 4 residues within 4Å: Chain A: N.122, W.123, R.125, D.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.125, A:D.126

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain C: N.791, D.832, W.836 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.832 Water bridges: C:W.836 GOL.5: 5 residues within 4Å: Chain C: S.917, P.919, Y.921, Q.928, T.930 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.917, C:Y.921, C:Q.928, C:G.929

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

CL.6: 2 residues within 4Å: Chain C: S.148, Q.202 Ligand excluded by PLIP

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

NA.7: 6 residues within 4Å: Chain C: Y.410, W.455, G.458, S.459, Y.502, Q.506 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sui, M. et al., Cancer Therapy with Nanoparticle-Medicated Intracellular Expression of Peptide CRM1-Inhibitor. Int J Nanomedicine (2021)

Release Date

2019-06-19

Peptides

GTP-binding nuclear protein Ran: A
Ran-specific GTPase-activating protein 1: B
Exportin-1: C
MVM NES mutant Nm12: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GTP-binding nuclear protein Ran

Ran-specific GTPase-activating protein 1

Exportin-1

MVM NES mutant Nm12

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