SMTL ID : 4hb0.1

Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1(K541Q,K542Q,R543S,K545Q,K548Q,K579Q)-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-oligomer

Ligands

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 26 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, A.67, G.68, Q.69, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:G.20, A:T.21, A:T.21, A:G.22, A:K.23, 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.42, A:G.68, A:N.122, A:K.123, A:K.123, A:A.151, A:K.152 Water bridges: A:V.40, A:Q.69, A:Q.69, A:K.152 Salt bridges: A:D.125 pi-Stacking: A:F.35, A:F.35

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x LBF: Leptomycin B(Covalent)

LBF.3: 15 residues within 4Å: Chain C: K.490, V.494, I.497, K.498, L.501, C.504, Q.513, A.517, I.520, H.534, F.537, T.540, V.541, Q.544, F.548 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.494, C:I.497, C:L.501, C:I.520, C:I.520, C:T.540, C:V.541, C:Q.544, C:F.548 Hydrogen bonds: C:Q.513 Salt bridges: C:K.490, C:H.534

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

CL.4: 2 residues within 4Å: Chain C: T.972, E.974 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain C: K.532, K.570, C.571, Y.573 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain C: P.63, Q.64, N.115, L.116 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain C: R.229 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Q. et al., Nuclear export inhibition through covalent conjugation and hydrolysis of Leptomycin B by CRM1. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-01-09

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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