SMTL ID : 1ek0.1

GPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.17, T.35 Ligands: GNP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.1, H2O.1

1 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 3 residues within 4Å: Chain A: E.49, H.50 Ligands: GDP.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.50, H2O.1, H2O.6, H2O.6, H2O.6

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

GNP.3: 23 residues within 4Å: Chain A: A.12, A.13, V.14, G.15, K.16, S.17, S.18, F.28, A.29, E.30, K.32, P.34, T.35, A.60, G.61, Q.62, N.116, K.117, D.119, S.149, A.150, K.151 Ligands: MG.1 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:A.13, A:V.14, A:G.15, A:K.16, A:K.16, A:S.17, A:S.18, A:S.18, A:A.29, A:T.35, A:T.35, A:G.61, A:N.116, A:K.117, A:K.117, A:A.150, A:K.151 Water bridges: A:S.17, A:E.30, A:E.30, A:E.30, A:E.33, A:Q.62, A:Q.62 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28

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

GDP.4: 6 residues within 4Å: Chain A: I.47, N.48, H.50, E.165, L.169 Ligands: NI.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.165 Water bridges: A:N.48, A:E.165, A:L.169, A:L.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esters, H. et al., High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis. J.Mol.Biol. (2000)

Release Date

2000-04-17

Peptides

PROTEIN (GTP-BINDING PROTEIN YPT51): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PROTEIN (GTP-BINDING PROTEIN YPT51)