SMTL ID : 3tpn.1

Crystal structure of M-PMV dUTPASE complexed with dUPNPP, substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-trimer

Ligands

3 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.1: 15 residues within 4Å: Chain A: G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105 Chain C: A.34, R.79, S.80, S.81, Q.123 Ligands: MG.2 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:R.79, C:R.79, C:S.80, C:S.80, C:S.81, C:Q.123, A:D.95, A:K.103, A:K.103 Water bridges: C:S.38, C:R.120, C:R.120, C:R.120, A:Y.98, A:M.105 Salt bridges: C:R.79 Hydrophobic interactions: A:I.94, A:Y.98 DUP.5: 15 residues within 4Å: Chain A: A.34, R.79, S.80, S.81, Q.123 Chain B: G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105 Ligands: MG.6 18 PLIP interactions: 11 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.79, A:R.79, A:S.80, A:S.80, A:S.81, A:Q.123, B:D.95, B:K.103, B:K.103 Water bridges: A:S.38, A:R.120, A:R.120, A:R.120, B:Y.98, B:M.105 Salt bridges: A:R.79 Hydrophobic interactions: B:I.94, B:Y.98 DUP.9: 15 residues within 4Å: Chain B: A.34, R.79, S.80, S.81, Q.123 Chain C: G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105 Ligands: MG.10 18 PLIP interactions: 11 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:R.79, B:R.79, B:S.80, B:S.80, B:S.81, B:Q.123, C:D.95, C:K.103, C:K.103 Water bridges: B:S.38, B:R.120, B:R.120, B:R.120, C:Y.98, C:M.105 Salt bridges: B:R.79 Hydrophobic interactions: C:I.94, C:Y.98

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: DUP.1 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: DUP.5 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: DUP.9 No protein-ligand interaction detected (PLIP)

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 14 residues within 4Å: Chain A: Q.88, V.89, Y.90, P.91 Chain B: Q.88, V.89, Y.90, P.91 Chain C: Q.88, V.89, Y.90, P.91 Ligands: TRS.7, TRS.11 7 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:Q.88, C:Q.88, A:Q.88 Water bridges: B:V.89, C:V.89, C:V.89, A:V.89 TRS.7: 14 residues within 4Å: Chain A: Q.88, V.89, Y.90, P.91 Chain B: Q.88, V.89, Y.90, P.91 Chain C: Q.88, V.89, Y.90, P.91 Ligands: TRS.3, TRS.11 7 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: B:Q.88, C:Q.88, A:Q.88 Water bridges: B:V.89, C:V.89, A:V.89, A:V.89 TRS.11: 14 residues within 4Å: Chain A: Q.88, V.89, Y.90, P.91 Chain B: Q.88, V.89, Y.90, P.91 Chain C: Q.88, V.89, Y.90, P.91 Ligands: TRS.3, TRS.7 7 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:Q.88, C:Q.88, A:Q.88 Water bridges: B:V.89, B:V.89, C:V.89, A:V.89

3 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.4: 5 residues within 4Å: Chain A: C.44, S.45, T.46, G.63, G.118 No protein-ligand interaction detected (PLIP) DTT.8: 5 residues within 4Å: Chain B: C.44, S.45, T.46, G.63, G.118 No protein-ligand interaction detected (PLIP) DTT.12: 5 residues within 4Å: Chain C: C.44, S.45, T.46, G.63, G.118 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barabas, O. et al., Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion. To be Published

Release Date

2011-10-12

Peptides

DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE

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