SMTL ID : 2dby.1

Crystal structure of the GTP-binding protein YchF in complexed with GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

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

GDP.1: 15 residues within 4Å: Chain A: L.9, P.10, N.11, V.12, G.13, K.14, S.15, T.16, R.108, F.110, N.209, V.210, S.242, A.243, R.244 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:L.9, A:N.11, A:V.12, A:G.13, A:K.14, A:S.15, A:S.15, A:T.16, A:T.16, A:R.108, A:R.108, A:N.209, A:A.243, A:R.244 Water bridges: A:S.242 pi-Cation interactions: A:F.110

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: H.105, A.128, V.131, E.132, V.204, Y.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.105 FMT.3: 4 residues within 4Å: Chain A: I.313, M.317, Y.363, V.364 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.364 FMT.4: 7 residues within 4Å: Chain A: A.28, A.29, N.30, P.44, P.68, T.69, H.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.29, A:N.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kukimoto-Niino, M. et al., Crystal structure of the GTP-binding protein YchF in complexed with GDP. To be Published

Release Date

2006-06-16

Peptides

GTP-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTP-binding protein

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