SMTL ID : 4nhk.1

Crystal structure of Tpa1p from Saccharomyces cerevisiae, termination and polyadenylation protein 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.162, D.164, H.230 Ligands: PD2.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.162, A:D.164, A:H.230, H2O.1

1 x PD2: PYRIDINE-2,4-DICARBOXYLIC ACID(Non-covalent)

PD2.2: 13 residues within 4Å: Chain A: Y.153, L.159, H.162, D.164, I.174, H.230, V.232, S.243, Q.245, W.247 Ligands: MN.1, GOL.3, GOL.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.159, A:I.174, A:V.232, A:Q.245 Hydrogen bonds: A:N.151, A:S.243 Water bridges: A:R.169 Salt bridges: A:H.162

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Y.91, Q.95, N.151, L.159 Ligands: PD2.2, GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.151, A:N.151 GOL.4: 8 residues within 4Å: Chain A: I.90, L.159, H.162, D.164, R.169, W.247 Ligands: PD2.2, GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.169, A:R.169 Water bridges: A:D.164 GOL.5: 3 residues within 4Å: Chain A: Y.425, R.426, N.427 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.427 Water bridges: A:R.426, A:N.427, A:D.433, A:D.433, A:D.433 GOL.6: 9 residues within 4Å: Chain A: R.292, F.522, N.523, L.526, K.527, I.532, I.533, D.534, D.634 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.292, A:N.523, A:D.534, A:D.534

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horita, S. et al., Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases. Structure (2015)

Release Date

2014-11-19

Peptides

PKHD-type hydroxylase TPA1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PKHD-type hydroxylase TPA1

Related Entries With Identical Sequence