SMTL ID : 8hq4.1

B27 in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 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.3

5 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.8: 7 residues within 4Å: Chain C: I.356, E.357, E.358, R.359, F.362, N.400, V.402 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.356, C:E.358, C:R.359, C:N.400 GOL.9: 6 residues within 4Å: Chain C: M.320, T.323, A.327, T.364, D.367, Y.368 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.364 GOL.10: 2 residues within 4Å: Chain C: D.88, H.89 No protein-ligand interaction detected (PLIP) GOL.11: 6 residues within 4Å: Chain C: Q.283, L.286, Q.287, E.341, L.342, N.345 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.286, C:E.341, C:N.345 Water bridges: C:L.342

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

GTP.3: 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, L.69, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.1 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:G.20, 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:Y.39, 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:T.24, A:V.40, A:V.40, A:T.42, 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

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

DMS.4: 5 residues within 4Å: Chain A: W.163, R.166, P.172 Chain C: A.307, Q.312 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.312 DMS.7: 5 residues within 4Å: Chain C: W.51, L.77, K.81, L.84, L.85 No protein-ligand interaction detected (PLIP) DMS.12: 2 residues within 4Å: Chain C: N.791, D.832 No protein-ligand interaction detected (PLIP)

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

CL.5: 4 residues within 4Å: Chain C: A.327, R.328, R.330, A.331 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain C: R.80 Ligand excluded by PLIP

1 x M9R: 3-[(4-fluorophenyl)carbonylamino]-4-[4-[3-(trifluoromethyl)phenyl]piperazin-1-yl]benzoic acid(Non-covalent)

M9R.13: 11 residues within 4Å: Chain C: L.481, I.500, M.501, V.504, N.516, F.517, T.520, V.521, K.524, L.525, F.528 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.481, C:I.500, C:K.524 Hydrogen bonds: C:N.516 Water bridges: C:N.516

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lei, Y. et al., B27 in complex with CRM1-Ran-RanBP1. To Be Published

Release Date

2023-12-20

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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