SMTL ID : 5hci.5 (4 other biounits)

GPN-loop GTPase Npa3 in complex with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 15 residues within 4Å: Chain A: M.10, G.12, S.13, G.14, K.15, T.16, T.17, N.172, K.173, D.175, V.176, S.228, S.229, F.230 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.12, A:S.13, A:G.14, A:K.15, A:T.16, A:T.17, A:T.17, A:N.172, A:K.173, A:K.173, A:S.229, A:F.230 Water bridges: A:T.16 Salt bridges: A:K.15, A:D.175 pi-Stacking: A:F.230 pi-Cation interactions: A:F.230 GDP.3: 15 residues within 4Å: Chain B: M.10, G.12, S.13, G.14, K.15, T.16, T.17, N.172, K.173, D.175, V.176, S.228, S.229, F.230 Ligands: MG.4 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.12, B:S.13, B:G.14, B:K.15, B:T.16, B:T.17, B:T.17, B:N.172, B:K.173, B:K.173, B:S.229, B:F.230 Water bridges: B:T.16, B:T.16, B:T.16, B:D.105 Salt bridges: B:K.15, B:D.175 pi-Stacking: B:F.230 pi-Cation interactions: B:F.230

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.16 Ligands: GDP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.16, H2O.1, H2O.1, H2O.1 MG.4: 2 residues within 4Å: Chain B: T.16 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.16, H2O.1, H2O.1, H2O.1, H2O.2

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain B: D.247, Q.251 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.247 GOL.6: 1 residues within 4Å: Chain B: Q.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niesser, J. et al., Structure of GPN-Loop GTPase Npa3 and Implications for RNA Polymerase II Assembly. Mol.Cell.Biol. (2015)

Release Date

2016-01-20

Peptides

GPN-loop GTPase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

GPN-loop GTPase 1

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