SMTL ID : 4nhy.1 (5 other biounits)

Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.175, D.177, H.238 Ligands: GOL.2, PD2.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.175, A:D.177, A:H.238, H2O.1

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: L.115, L.172, H.175 Ligands: MN.1, PD2.3 No protein-ligand interaction detected (PLIP)

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

PD2.3: 13 residues within 4Å: Chain A: L.172, H.175, D.177, I.187, Y.189, L.202, H.238, V.240, R.250, S.252, W.256 Ligands: MN.1, GOL.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.172, A:I.187, A:L.202, A:V.240 Hydrogen bonds: A:Y.189, A:S.252, A:S.254 Water bridges: A:Y.166, A:Y.166 Salt bridges: A:H.175, A:R.250

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

2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1

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