SMTL ID : 2qcm.1

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to 6-hydroxymethyl-UMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

2 x JW5: 6-(HYDROXYMETHYL)URIDINE 5'-(DIHYDROGEN PHOSPHATE)(Non-covalent)

JW5.1: 17 residues within 4Å: Chain A: S.37, D.39, K.61, H.63, N.92, 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 20 PLIP interactions: 3 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:D.97, B:T.101, B:T.101, A:S.37, A:D.39, A:K.61, A:N.92, A:N.92, A:S.152, A:S.152, A:S.152, A:Q.210, A:Y.212, A:G.230, A:R.231 Hydrophobic interactions: A:P.197 Water bridges: A:G.198, A:G.198, A:G.232 Salt bridges: A:R.231 JW5.2: 17 residues within 4Å: Chain A: D.97, I.98, T.101 Chain B: S.37, D.39, K.61, H.63, N.92, M.151, S.152, P.197, Q.210, Y.212, I.228, V.229, G.230, R.231 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.197 Hydrogen bonds: B:S.37, B:K.61, B:N.92, B:N.92, B:S.152, B:S.152, B:S.152, B:Q.210, B:G.230, B:R.231, A:D.97, A:T.101 Water bridges: B:G.198, B:G.198, B:G.232 Salt bridges: B:R.231

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
A

Uridine 5'-monophosphate synthase (UMP synthase)

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