SMTL ID : 7dbg.1

Yeast CRM1e (apo) in complex with Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 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.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.42, H2O.1, H2O.1

2 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: 6 residues within 4Å: Chain C: I.356, E.357, E.358, R.359, F.362, N.400 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.356, C:E.358, C:N.400

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, V.40, A.41, T.42, A.67, G.68, L.69, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.1 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.20, A:T.21, A:G.22, A:K.23, A:T.24, A:T.25, A:T.25, A:E.36, A:Y.39, A:T.42, A:G.68, A:N.122, A:K.123, A:K.123, A:S.150, A:A.151, A:K.152 Water bridges: A:T.24, 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

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

CL.4: 3 residues within 4Å: Chain A: P.49, L.50, V.51 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain C: K.512, H.554 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain C: A.327, R.328, N.329, R.330, A.331 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain C: R.80 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain C: K.186, S.190 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain C: P.823 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain C: Q.575 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: T.889, A.947 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain C: E.360 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain C: T.650 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: A.133, I.136 Chain C: E.360, K.363 Ligand excluded by PLIP

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

DMS.9: 6 residues within 4Å: Chain C: S.208, S.210, F.245, S.248, D.250, T.251 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.248 Salt bridges: C:D.250 DMS.10: 5 residues within 4Å: Chain C: W.51, L.77, K.81, L.84, L.85 No protein-ligand interaction detected (PLIP)

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.19: 10 residues within 4Å: Chain A: V.137, R.140, K.141 Chain C: M.320, T.323, T.324, A.327, T.364, D.367, Y.368 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Water bridges: A:K.141 Salt bridges: A:R.140, A:K.141 Hydrogen bonds: C:T.323

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

2021-09-29

Peptides

GTP-binding nuclear protein Ran: A
YRB1 isoform 1: B
CRM1 isoform 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GTP-binding nuclear protein Ran

YRB1 isoform 1

CRM1 isoform 1

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