SMTL ID : 8hq5.1

G6 in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.24, T.42, D.65 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: 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

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

GTP.3: 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, 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.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:V.40, A:V.40, A:V.40, A:T.42, A:D.65, 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

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

CL.4: 2 residues within 4Å: Chain A: P.49, V.51 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain C: K.512, H.554 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain C: R.328, R.330, A.331 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain C: R.80, H.950 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: E.784, L.822 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: T.889, A.947 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: Q.316, E.360 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: N.646, T.650 Ligand excluded by PLIP CL.17: 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: 4 residues within 4Å: Chain C: S.208, 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: 4 residues within 4Å: Chain C: W.51, K.81, L.84, L.85 No protein-ligand interaction detected (PLIP)

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

MPO.18: 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 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:R.140 Hydrogen bonds: C:T.323

1 x MBI: 3-[(4-bromophenyl)carbonylamino]-4-[4-(5-chloranyl-2-methyl-phenyl)piperazin-1-yl]benzoic acid(Non-covalent)

MBI.19: 15 residues within 4Å: Chain C: V.473, I.477, L.481, I.500, M.501, V.504, Y.507, F.510, L.511, F.517, T.520, V.521, K.524, L.525, F.528 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.473, C:I.477, C:I.477, C:L.481, C:I.500, C:F.510, C:L.511, C:F.517, C:V.521, C:K.524, C:F.528 Salt bridges: C:K.478

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Q. et al., F1 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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