SMTL ID : 5bxq.1

Structure of the NTF2:RanGDP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-3-mer

Ligands

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

GDP.1: 17 residues within 4Å: Chain C: D.18, G.19, G.20, T.21, G.22, K.23, T.24, T.25, E.70, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: 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 GDP.3: 18 residues within 4Å: Chain D: D.18, G.19, G.20, T.21, G.22, K.23, T.24, T.25, E.70, K.71, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.4 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:G.20, D:T.21, D:T.21, D:G.22, D:K.23, D:T.24, D:T.25, D:T.25, D:N.122, D:K.123, D:K.123, D:A.151, D:K.152, D:K.152 Water bridges: D:K.23, D:K.23, D:K.23, D:T.24, D:T.24 Salt bridges: D:K.23, D:D.125 GDP.7: 17 residues within 4Å: Chain E: D.18, G.19, G.20, T.21, G.22, K.23, T.24, T.25, E.70, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.5 23 PLIP interactions: 23 interactions with chain E Hydrogen bonds: E:G.20, E:T.21, E:G.22, E:K.23, E:T.24, E:T.24, E:T.25, E:T.25, E:E.70, E:E.70, E:N.122, E:K.123, E:K.123, E:A.151, E:K.152, E:K.152 Water bridges: E:T.24, E:T.24, E:D.65, E:T.66, E:E.70 Salt bridges: E:K.23, E:D.125

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain C: T.24 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.24, H2O.5, H2O.6, H2O.6, H2O.6 MG.4: 3 residues within 4Å: Chain D: T.24, T.66 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.24, H2O.8, H2O.9, H2O.9, H2O.9 MG.5: 2 residues within 4Å: Chain E: T.24 Ligands: GDP.7 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:T.24, H2O.11, H2O.11, H2O.12, H2O.12

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

SO4.6: 5 residues within 4Å: Chain E: H.30, T.32, H.53, P.180, A.181 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.32, E:A.181 Water bridges: E:H.30, E:H.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stewart, M. et al., Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran. J.Mol.Biol. (1998)

Release Date

2015-07-01

Peptides

Nuclear transport factor 2: AB
GTP-binding nuclear protein Ran: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Nuclear transport factor 2

GTP-binding nuclear protein Ran

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