SMTL ID : 3ewu.1

D312N mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-acetyl-UMP, covalent adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: K.22, I.79, A.82, K.83, F.87, L.88, D.118 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.22, A:K.22, A:A.82, A:K.83, A:F.87

2 x UEP: 6-ethyluridine 5'-phosphate(Covalent)

UEP.2: 18 residues within 4Å: Chain A: S.37, D.39, K.61, N.92, K.94, N.121, M.151, S.152, I.181, P.197, Q.210, Y.212, V.229, G.230, R.231 Chain B: D.97, I.98, T.101 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.94, A:I.181, A:P.197 Hydrogen bonds: A:S.37, A:D.39, A:K.61, A:N.92, A:S.152, A:S.152, A:S.152, A:Q.210, A:Y.212, A:Y.212, A:G.230, A:R.231, B:T.101 Water bridges: A:G.198, A:G.198, A:G.232 Salt bridges: A:R.231 UEP.4: 18 residues within 4Å: Chain A: D.97, I.98, T.101 Chain B: S.37, D.39, K.61, N.92, K.94, N.121, M.151, S.152, I.181, P.197, Q.210, Y.212, V.229, G.230, R.231 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.94, B:I.181, B:P.197 Hydrogen bonds: B:S.37, B:D.39, B:K.61, B:N.92, B:S.152, B:S.152, B:S.152, B:Q.210, B:Y.212, B:Y.212, B:G.230, B:R.231, A:T.101 Water bridges: B:G.198, B:G.198 Salt bridges: B:R.231

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

SO4.3: 4 residues within 4Å: Chain B: S.128, K.132, E.172, H.173 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.128, B:S.128, B:E.172 Salt bridges: B:K.132, B:H.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heinrich, D. et al., Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase. Chemistry (2009)

Release Date

2009-04-07

Peptides

Orotidine-5'-phosphate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Orotidine-5'-phosphate decarboxylase

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