SMTL ID : 5uwi.1

Crystal Structure of HDAC5 NES Peptide in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 27 residues within 4Å: Chain A: D.39, G.40, G.41, T.42, G.43, K.44, T.45, T.46, F.56, E.57, K.58, K.59, Y.60, V.61, A.62, T.63, A.88, G.89, Q.90, N.143, K.144, D.146, I.147, S.171, A.172, K.173 Ligands: MG.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:G.41, A:T.42, A:T.42, A:G.43, A:K.44, A:K.44, A:T.45, A:T.46, A:T.46, A:E.57, A:Y.60, A:Y.60, A:T.63, A:T.63, A:T.87, A:G.89, A:N.143, A:K.144, A:K.144, A:S.171, A:A.172, A:K.173 Water bridges: A:T.45, A:V.61, A:Q.90 Salt bridges: A:D.146 pi-Stacking: A:F.56, A:F.56

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.45, T.63, D.86 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.45, A:T.63, H2O.1, H2O.2

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: D.39, N.121, N.124, W.125, R.127, D.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.124, A:D.128 Water bridges: A:N.124 GOL.4: 7 residues within 4Å: Chain C: R.80, K.81, H.971, I.1005, K.1006, E.1007, V.1008 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.80, C:R.80, C:H.971 Water bridges: C:H.971 GOL.5: 5 residues within 4Å: Chain C: E.194, R.230, Y.231, E.234, T.235 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.194, C:R.230, C:E.234, C:E.234 GOL.6: 5 residues within 4Å: Chain C: L.808, N.812, D.853, A.854, W.857 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.812, C:N.812

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fung, H.Y. et al., Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals. Elife (2017)

Release Date

2017-03-22

Peptides

GTP-binding nuclear protein Ran: A
Ran-specific GTPase-activating protein 1: B
Exportin-1: C
Histone deacetylase 5: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GTP-binding nuclear protein Ran

Ran-specific GTPase-activating protein 1

Exportin-1

Histone deacetylase 5

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