SMTL ID : 2qch.1

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to 5-iodo-UMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 7 residues within 4Å: Chain A: K.61, D.92, K.94, N.121, I.181 Ligands: 5IU.2, UMP.3 Ligand excluded by PLIP IOD.4: 6 residues within 4Å: Chain B: D.92, K.94, N.121, I.181 Ligands: 5IU.5, UMP.6 Ligand excluded by PLIP

2 x 5IU: 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

5IU.2: 20 residues within 4Å: Chain A: S.37, D.39, K.61, H.63, D.92, K.94, I.148, M.151, S.152, P.197, G.198, Q.210, Y.212, G.230, R.231 Chain B: D.97, I.98, T.101 Ligands: IOD.1, UMP.3 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.37, A:K.61, A:S.152, A:S.152, A:S.152, A:G.198, A:Q.210, A:G.230, A:R.231 Water bridges: A:G.232 Salt bridges: A:R.231 Hydrophobic interactions: B:I.98 5IU.5: 20 residues within 4Å: Chain A: D.97, I.98, T.101 Chain B: S.37, D.39, K.61, H.63, D.92, K.94, I.148, M.151, S.152, P.197, Q.210, Y.212, V.229, G.230, R.231 Ligands: IOD.4, UMP.6 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.37, B:K.61, B:S.152, B:S.152, B:S.152, B:Q.210, B:G.230, B:R.231 Water bridges: B:G.198, B:G.198, B:G.232, A:T.101 Salt bridges: B:R.231 Hydrophobic interactions: A:I.98

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.3: 19 residues within 4Å: Chain A: S.37, D.39, K.61, H.63, D.92, K.94, M.151, S.152, P.197, Q.210, Y.212, V.229, G.230, R.231 Chain B: D.97, I.98, T.101 Ligands: IOD.1, 5IU.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.197, B:I.98 Hydrogen bonds: A:S.37, A:K.61, A:S.152, A:S.152, A:S.152, A:Q.210, A:G.230, A:R.231 Water bridges: A:G.232 Salt bridges: A:R.231 UMP.6: 18 residues within 4Å: Chain A: D.97, I.98, T.101 Chain B: S.37, D.39, K.61, H.63, D.92, K.94, M.151, S.152, P.197, Q.210, Y.212, G.230, R.231 Ligands: IOD.4, 5IU.5 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.197, A:I.98 Hydrogen bonds: B:S.37, B:K.61, B:D.92, B:S.152, B:S.152, B:S.152, B:Q.210, B:G.230, B:R.231 Water bridges: B:G.198, B:G.198, B:G.232, 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
B

Uridine 5'-monophosphate synthase (UMP synthase)

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