SMTL ID : 5yst.1

RanM189D in complex with RanBP1-CRM1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.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, T.66, A.67, G.68, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:D.18, 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:E.36, 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: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

2 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 MG.4: 1 residues within 4Å: Chain A: E.186 No protein-ligand interaction detected (PLIP)

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

EDO.3: 4 residues within 4Å: Chain A: N.100, N.103, W.104, D.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.100, A:N.103, A:D.107

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

CL.5: 4 residues within 4Å: Chain A: R.129, K.132, A.133, K.134 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: T.972, S.973, E.974 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain C: K.570, C.571, K.572, Y.573 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain C: P.63, Q.64, N.115 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain C: R.229 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain C: D.852, E.903 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain C: N.811, W.856 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.811 Water bridges: C:N.811 GOL.12: 3 residues within 4Å: Chain C: G.687, Y.691 Ligands: GOL.13 No protein-ligand interaction detected (PLIP) GOL.13: 4 residues within 4Å: Chain C: Y.691, N.692, Q.695 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Y.691, C:Q.695 GOL.14: 4 residues within 4Å: Chain C: K.180, H.183, D.1010, D.1013 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.1013 Water bridges: C:A.179, C:H.183, C:D.1013 GOL.15: 5 residues within 4Å: Chain C: I.100, L.124, S.146, N.156, N.157 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Q. et al., RanM189D 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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