SMTL ID : 5xc5.1

Crystal structure of Acanthamoeba polyphaga mimivirus Rab GTPase in complex with GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 21 residues within 4Å: Chain A: S.13, S.14, G.15, V.16, G.17, K.18, S.19, S.20, V.34, P.36, T.37, A.63, G.64, N.119, K.120, D.122, I.123, S.150, S.151, F.152 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.13, A:G.15, A:V.16, A:G.17, A:K.18, A:S.19, A:S.20, A:S.20, A:T.37, A:G.64, A:N.119, A:K.120, A:K.120, A:S.150, A:S.151, A:S.151 Water bridges: A:T.37, A:T.37, A:L.65 Salt bridges: A:K.18, A:K.18, A:D.122

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.19, T.37 Ligands: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.19, A:T.37, H2O.2, H2O.2

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: L.65, E.66, R.67 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.65, A:E.66 Hydrogen bonds: A:E.66, A:R.67 Salt bridges: A:R.67 ACT.4: 1 residues within 4Å: Chain A: R.140 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.140 ACT.5: 8 residues within 4Å: Chain A: H.23, F.27, R.29, K.30, I.31, S.32, N.33, V.34 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.32, A:N.33 Salt bridges: A:H.23, A:R.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ku, B. et al., Crystal structures of two forms of the Acanthamoeba polyphaga mimivirus Rab GTPase. Arch. Virol. (2017)

Release Date

2017-10-25

Peptides

Probable Rab-related GTPase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable Rab-related GTPase