SMTL ID : 2qcl.1

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to OMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x OMP: OROTIDINE-5'-MONOPHOSPHATE(Non-covalent)

OMP.1: 18 residues within 4Å: Chain A: S.37, K.61, H.63, N.92, K.94, N.121, M.151, S.152, P.197, Q.210, Y.212, I.228, V.229, G.230, R.231 Chain B: D.97, I.98, T.101 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.197 Hydrogen bonds: A:S.37, A:S.37, A:K.61, A:S.152, A:S.152, A:S.152, A:Q.210, A:Y.212, A:G.230, A:R.231, B:T.101 Water bridges: A:G.198, A:V.199, A:V.199, A:G.232 Salt bridges: A:K.61, A:K.94, A:R.231 OMP.3: 18 residues within 4Å: Chain A: D.97, I.98, T.101 Chain B: S.37, K.61, H.63, N.92, K.94, N.121, M.151, S.152, P.197, Q.210, Y.212, I.228, V.229, G.230, R.231 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.197 Hydrogen bonds: B:S.37, B:S.37, B:K.61, B:S.152, B:S.152, B:S.152, B:Q.210, B:Y.212, B:G.230, B:R.231, A:T.101 Water bridges: B:K.94, B:G.198, B:G.198, B:V.199, B:G.232 Salt bridges: B:K.61, B:K.94, B:R.231

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.22, A.82, K.83, F.87, L.88, D.118 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.22, A:K.83, A:F.87, A:D.118 Water bridges: A:D.118, A:D.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wittmann, J.G. et al., Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design. Structure (2008)

Release Date

2007-11-06

Peptides

Uridine 5'-monophosphate synthase (UMP synthase): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uridine 5'-monophosphate synthase (UMP synthase)

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