SMTL ID : 2gwn.1

The structure of putative dihydroorotase from Porphyromonas gingivalis.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: Q.66, K.152, H.184, H.242 Ligands: ZN.2, CAC.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.184, A:H.242, H2O.362 ZN.2: 5 residues within 4Å: Chain A: Q.66, H.68, K.152, D.316 Ligands: ZN.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.68, A:D.316, H2O.362

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.3: 9 residues within 4Å: Chain A: H.68, N.100, K.152, F.154, S.157, S.158, H.184, N.289 Ligands: ZN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.157, A:S.157 Water bridges: A:N.289 CAC.4: 3 residues within 4Å: Chain A: R.9, L.39, A.41 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.9, A:R.9, A:N.10, A:L.39

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

CL.5: 4 residues within 4Å: Chain A: P.337, L.338, H.341, S.411 Ligand excluded by PLIP

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain A: D.120, R.442 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.442, A:R.442 Salt bridges: A:R.442 SO4.7: 3 residues within 4Å: Chain A: V.445, H.446, P.447 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.446 SO4.8: 2 residues within 4Å: Chain A: S.1, T.444 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.1, A:S.1 Water bridges: A:V.445, A:V.445, A:V.445 SO4.9: 3 residues within 4Å: Chain A: Y.221, R.222, A.225 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.221 Salt bridges: A:R.222 SO4.10: 2 residues within 4Å: Chain A: R.298 Ligands: GOL.14 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.298, A:R.298, A:R.302, A:Q.352, A:Q.352, A:Q.352 Salt bridges: A:R.298

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.11: 6 residues within 4Å: Chain A: S.1, N.2, C.430, R.442, P.443, T.444 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.1, A:R.442, A:T.444 BME.12: 5 residues within 4Å: Chain A: I.137, I.140, K.141, E.176, C.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.176

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: L.321, L.322, C.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.322 GOL.14: 5 residues within 4Å: Chain A: W.273, L.349, Q.352, F.416 Ligands: SO4.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.273, A:R.298, A:Q.352, A:Q.352 Water bridges: A:R.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuff, M.E. et al., The structure of putative dihydroorotase from Porphyromonas gingivalis. To be Published

Release Date

2006-06-06

Peptides

dihydroorotase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

dihydroorotase