SMTL ID : 5ysu.1

Plumbagin in complex with CRM1-RanM189D-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.1: 28 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, T.66, A.67, G.68, Q.69, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:G.20, A:T.21, 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:T.42, A:T.42, A:T.66, A:G.68, A:Q.69, A:N.122, A:K.123, A:K.123, A:A.151, A:K.152 Water bridges: A:T.24, A:V.40, A:Q.69, A:Q.69 Salt bridges: A:K.23, A:K.23, 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: GTP.1 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 CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.129, A.133 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain C: R.80 Ligand excluded by PLIP

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 3 residues within 4Å: Chain A: N.103, W.104, D.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.103, A:R.106 Water bridges: A:W.104 NO3.5: 5 residues within 4Å: Chain A: T.93, S.94, R.95, K.130 Chain C: R.864 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.864, A:R.95 Water bridges: A:S.94, A:V.96 NO3.10: 4 residues within 4Å: Chain C: V.939, P.940, S.952, N.953 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.953, C:N.953 NO3.11: 3 residues within 4Å: Chain C: N.812, D.853, W.857 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.812, C:D.853

2 x F2X: (2~{R})-2-methyl-5-oxidanyl-2,3-dihydronaphthalene-1,4-dione(Covalent)

F2X.6: 7 residues within 4Å: Chain C: I.929, S.930, Y.933, Q.954, T.985, K.986, C.988 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.933, C:Y.933, C:Y.933, C:Y.933, C:Q.954 Hydrogen bonds: C:I.929 F2X.7: 9 residues within 4Å: Chain C: S.148, V.152, C.155, L.199, Q.202, V.203, Q.206, G.207, L.212 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.199, C:V.203, C:L.212 Hydrogen bonds: C:Q.202

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

NA.9: 5 residues within 4Å: Chain C: Y.233, V.262, I.267, T.278, F.281 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.233, C:Y.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Q. et al., RanL182A in complex with RanBP1-CRM1. To Be Published

Release Date

2018-11-21

Peptides

GTP-binding nuclear protein Ran: A
Ran-specific GTPase-activating protein 1: B
Exportin-1,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,Exportin-1

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