SMTL ID : 4phg.1

Crystal structure of Ypt7 covalently modified with GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.24, T.42, D.66 Ligands: 2UJ.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.42, H2O.1, H2O.1

1 x 2UJ: N-[3-(propanoylamino)propyl]guanosine 5'-(tetrahydrogen triphosphate)(Covalent)

2UJ.2: 24 residues within 4Å: Chain A: D.18, S.19, G.20, V.21, G.22, K.23, T.24, S.25, Y.35, S.36, C.37, Q.38, Y.39, A.41, T.42, A.68, G.69, N.128, K.129, D.131, S.160, A.161, K.162 Ligands: MG.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.35 Hydrogen bonds: A:S.19, A:G.20, A:V.21, A:G.22, A:K.23, A:T.24, A:S.25, A:S.25, A:S.25, A:Y.35, A:C.37, A:T.42, A:G.69, A:N.128, A:K.129, A:K.129, A:D.131, A:A.161, A:K.162 Water bridges: A:T.24, A:T.24 Salt bridges: A:K.23, A:K.23 pi-Stacking: A:Y.35, A:Y.35

3 x YT3: YTTRIUM (III) ION(Non-covalent)

YT3.3: 1 residues within 4Å: Chain A: D.33 No protein-ligand interaction detected (PLIP) YT3.4: 2 residues within 4Å: Chain A: E.71, E.108 No protein-ligand interaction detected (PLIP) YT3.5: 1 residues within 4Å: Chain A: E.119 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wiegandt, D. et al., Locking GTPases covalently in their functional states. Nat Commun (2015)

Release Date

2014-05-28

Peptides

GTP-binding protein YPT7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTP-binding protein YPT7