SMTL ID : 4nhx.1

Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with N-oxalylglycine (NOG)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 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: OGA.3, GOL.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.175, A:D.177, A:H.238, H2O.2

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: Y.524, R.525, D.526, T.529 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.524, A:D.526

1 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.3: 12 residues within 4Å: Chain A: L.172, H.175, D.177, I.187, Y.189, L.202, H.238, V.240, R.250, W.256 Ligands: MN.1, GOL.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.254 Water bridges: A:Y.166, A:R.250, A:S.252, A:S.254 Salt bridges: A:H.175, A:R.250

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Y.116, H.175, R.182, W.256 Ligands: MN.1, OGA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.182 Water bridges: A:D.177

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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