SMTL ID : 2qcf.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-dimer

Ligands

2 x 5FU: 5-FLUORO-URIDINE-5'-MONOPHOSPHATE(Non-covalent)

5FU.1: 19 residues within 4Å: Chain A: S.37, D.39, K.61, H.63, N.92, K.94, M.151, S.152, I.181, 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: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.37, A:D.39, A:K.61, A:N.92, A:K.94, A:S.152, A:S.152, A:S.152, A:Q.210, A:Y.212, A:G.230, A:R.231, B:D.97, B:T.101, B:T.101 Water bridges: A:G.198, A:G.198, A:Q.200 Salt bridges: A:R.231 5FU.3: 19 residues within 4Å: Chain A: D.97, I.98, T.101 Chain B: S.37, D.39, K.61, H.63, N.92, K.94, M.151, S.152, I.181, P.197, Q.210, Y.212, I.228, V.229, G.230, R.231 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.37, B:K.61, B:N.92, B:K.94, 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:Q.200 Salt bridges: B:R.231

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: S.6, G.8, A.9, E.12, Q.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.6, A:S.6, A:E.12, A:Q.28 GOL.4: 5 residues within 4Å: Chain B: S.6, G.8, A.9, E.12, Q.28 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.6, B:S.6, B:E.12, B:Q.28

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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