SMTL ID : 2d4n.1

Crystal Structure of M-PMV dUTPase complexed with dUPNPP, substrate analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-trimer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: DUP.2 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: DUP.5 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: DUP.8 No protein-ligand interaction detected (PLIP)

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

DUP.2: 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.1 15 PLIP interactions: 6 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:I.94, A:Y.98 Hydrogen bonds: A:D.95, A:K.103, A:K.103, C:R.79, C:R.79, C:S.80, C:S.80, C:S.81, C:Q.123 Water bridges: A:M.105, C:S.81, C:S.81 Salt bridges: C:R.79 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.4 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:I.94, B:Y.98 Hydrogen bonds: B:D.95, B:K.103, B:K.103, A:R.79, A:R.79, A:S.80, A:S.80, A:S.81, A:Q.123 Water bridges: B:M.105, A:S.81, A:S.81 Salt bridges: A:R.79 DUP.8: 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.7 15 PLIP interactions: 9 interactions with chain B, 6 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.81, B:S.81, C:M.105 Salt bridges: B:R.79 Hydrophobic interactions: C:I.94, C:Y.98

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.6, TRS.9 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Water bridges: C:V.89, A:V.89, B:V.89, B:V.89 TRS.6: 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.9 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Water bridges: C:V.89, C:V.89, A:V.89, B:V.89 TRS.9: 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.6 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Water bridges: C:V.89, A:V.89, A:V.89, B:V.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nemeth-Pongracz, V. et al., Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins. Nucleic Acids Res. (2007)

Release Date

2006-11-21

Peptides

DU: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DU

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