SMTL ID : 4hb2.1

Crystal structure of CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

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:K.23, A:T.24, A:T.25, A:T.25, A:E.36, A:Y.39, A:T.42, 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:V.40, A:Q.69, A:Q.69 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.8, H2O.8

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.166, K.167, G.170, D.171, P.172 Chain C: A.306, Q.311 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.311 Water bridges: C:A.306, A:K.167 GOL.6: 6 residues within 4Å: Chain C: E.193, F.196, R.229, Y.230, E.233, T.234 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.193, C:E.193, C:R.229, C:E.233, C:E.233 GOL.7: 3 residues within 4Å: Chain C: L.807, N.811, W.856 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.811 Water bridges: C:N.811, C:D.852 GOL.12: 4 residues within 4Å: Chain C: H.534, W.535, N.536, F.537 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.536, C:N.536, C:F.537 Water bridges: C:W.535, C:W.535

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

EDO.4: 5 residues within 4Å: Chain A: N.100, N.103, W.104, R.106, D.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.100, A:N.103, A:R.106, A:D.107 Water bridges: A:R.106 EDO.8: 6 residues within 4Å: Chain C: V.931, Y.932, Q.953, L.956, S.957, T.984 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.928, C:S.957, C:S.957

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

CL.5: 5 residues within 4Å: Chain A: T.93, S.94, R.95, K.130 Chain C: R.863 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain C: T.972, S.973, E.974 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: K.570, C.571, K.572, Y.573 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: P.63, Q.64, N.115 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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