SMTL ID : 5hci.2 (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: 16 residues within 4Å: Chain A: M.10, A.11, 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 16 PLIP interactions: 16 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 Salt bridges: A:K.15, A:D.175 pi-Stacking: A:F.230 pi-Cation interactions: A:F.230 GDP.4: 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.5 19 PLIP interactions: 19 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.228, B:S.229, B:F.230 Water bridges: B:K.15, B:K.15 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: 4 residues within 4Å: Chain A: T.16, D.39, V.42 Ligands: GDP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.16, A:D.39, H2O.1, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: T.16, D.105 Ligands: GDP.4 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: D.223, V.224, E.237, C.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.223, A:V.224, A:E.237

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
C

B
B

GPN-loop GTPase 1

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