SMTL ID : 1t6c.1

Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 1 residues within 4Å: Chain A: Y.229 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.144, Q.145, G.146, S.149, E.151 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.144, A:G.146, A:E.151, H2O.4, H2O.4

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 7 residues within 4Å: Chain A: Q.145, G.146, G.147, G.148, S.149, G.169, I.170 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: G.169, V.171, N.172 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: Q.145, I.170, R.270 Ligand excluded by PLIP

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 4 residues within 4Å: Chain A: D.78, K.81, V.82, E.83 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.83 Water bridges: A:D.78 MPD.7: 4 residues within 4Å: Chain A: S.133, P.231, H.235, W.298 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.231, A:H.235, A:W.298 Water bridges: A:Q.232 MPD.8: 5 residues within 4Å: Chain A: T.250, E.253, I.254, R.262 Ligands: MPD.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.254 Water bridges: A:R.262, A:R.262 MPD.9: 4 residues within 4Å: Chain A: W.247, T.250, F.263 Ligands: MPD.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.247, A:W.247, A:F.263 Hydrogen bonds: A:T.250 MPD.10: 3 residues within 4Å: Chain A: E.139, K.156, R.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.139, A:R.161, A:R.161 MPD.11: 5 residues within 4Å: Chain A: Q.121, Y.125, L.128, S.307, K.311 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.125, A:L.128 Hydrogen bonds: A:Q.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kristensen, O. et al., Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family. Biochemistry (2004)

Release Date

2004-08-03

Peptides

exopolyphosphatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

exopolyphosphatase