SMTL ID : 4phf.1

Crystal structure of Ypt7 covalently modified with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x 2UH: N-[3-(propanoylamino)propyl]guanosine 5'-(trihydrogen diphosphate)(Covalent)

2UH.1: 17 residues within 4Å: Chain A: D.18, S.19, G.20, V.21, G.22, K.23, T.24, S.25, Y.35, C.37, N.128, K.129, D.131, S.160, A.161, K.162 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:K.162 Hydrogen bonds: A:G.20, A:V.21, A:G.22, A:K.23, A:T.24, A:S.25, A:S.25, A:Y.35, A:N.128, A:K.129, A:K.129, A:D.131, A:D.131, A:A.161, A:K.162 Water bridges: A:T.24 Salt bridges: A:K.23 pi-Stacking: A:Y.35

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.24 Ligands: 2UH.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.24, H2O.1, H2O.1, H2O.2, H2O.2

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 6 residues within 4Å: Chain A: R.29, A.164, I.165, N.166, V.167, D.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.167, A:D.168

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

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