SMTL ID : 3ch5.2 (1 other biounit)

The crystal structure of the RanGDP-Nup153ZnF2 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.24 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.24, H2O.1, H2O.2, H2O.2, H2O.2 MG.5: 2 residues within 4Å: Chain C: T.24 Ligands: GDP.7 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.24, H2O.4, H2O.5, H2O.5, H2O.5

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 10 residues within 4Å: Chain A: H.30, T.32, V.51, H.53, P.180, A.181 Chain C: T.32, P.180, A.181 Ligands: SO4.6 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:A.181, C:T.32, C:T.32, C:A.181 Water bridges: A:T.32, A:T.32, C:T.32 Salt bridges: A:H.30, A:H.53 SO4.6: 10 residues within 4Å: Chain A: T.32, P.180, A.181 Chain C: H.30, T.32, V.51, H.53, P.180, A.181 Ligands: SO4.2 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:A.181, A:T.32, A:T.32, A:A.181 Water bridges: C:T.32, C:T.32, A:T.32 Salt bridges: C:H.30, C:H.53

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 16 residues within 4Å: Chain A: D.18, G.19, G.20, T.21, G.22, K.23, T.24, T.25, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:D.18, 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.70, A:N.122, A:K.123, A:K.123, A:A.151, A:K.152, A:K.152 Water bridges: A:T.24, A:K.71 Salt bridges: A:K.23, A:D.125 GDP.7: 16 residues within 4Å: Chain C: D.18, G.19, G.20, T.21, G.22, K.23, T.24, T.25, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.5 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:D.18, C:G.20, C:T.21, C:G.22, C:K.23, C:T.24, C:T.24, C:T.25, C:T.25, C:E.70, C:N.122, C:K.123, C:K.123, C:A.151, C:K.152, C:K.152 Water bridges: C:T.24, C:K.71 Salt bridges: C:K.23, C:D.125

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain B: C.25, C.28, C.39, C.42 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.25, B:C.28, B:C.39, B:C.42 ZN.8: 4 residues within 4Å: Chain D: C.25, C.28, C.39, C.42 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.25, D:C.28, D:C.39, D:C.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schrader, N. et al., The Crystal Structure of the Ran-Nup153ZnF2 Complex: a General Ran Docking Site at the Nuclear Pore Complex. Structure (2008)

Release Date

2008-07-01

Peptides

GTP-binding nuclear protein Ran: AC
Fragment of Nuclear pore complex protein Nup153: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

GTP-binding nuclear protein Ran

Fragment of Nuclear pore complex protein Nup153

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