SMTL ID : 6mao.1

Crystal structure of Deoxyuridine 5'-triphosphate nucleotidohydrolase from Legionella pneumophila Philadelphia 1 in complex with dUMP (Deoxyuridine 5'-monophosphate)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

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

UMP.1: 12 residues within 4Å: Chain A: I.76, N.92, G.95, L.96, I.97, D.98, Y.101, E.104, L.105, K.106 Chain C: S.80 Ligands: MPD.2 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:I.97, A:Y.101 Hydrogen bonds: A:N.92, A:L.96, A:D.98, A:K.106, A:K.106 Water bridges: A:L.96, A:D.98, A:D.98, C:R.79, C:R.79, C:S.80, C:G.81, C:Q.127 UMP.4: 12 residues within 4Å: Chain A: S.80 Chain B: I.76, N.92, G.95, L.96, I.97, D.98, Y.101, E.104, L.105, K.106 Ligands: MPD.5 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.97, B:Y.101 Hydrogen bonds: B:N.92, B:L.96, B:D.98, B:K.106, B:K.106 Water bridges: B:L.96, B:D.98, B:D.98, A:R.79, A:R.79, A:S.80, A:G.81, A:Q.127 UMP.7: 12 residues within 4Å: Chain B: S.80 Chain C: I.76, N.92, G.95, L.96, I.97, D.98, Y.101, E.104, L.105, K.106 Ligands: MPD.8 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.97, C:Y.101 Hydrogen bonds: C:N.92, C:L.96, C:D.98, C:K.106, C:K.106 Water bridges: C:L.96, C:D.98, C:D.98, B:R.79, B:R.79, B:S.80, B:G.81, B:Q.127

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 5 residues within 4Å: Chain A: L.58 Chain C: S.80, H.84, K.85 Ligands: UMP.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.80, C:K.85 MPD.5: 5 residues within 4Å: Chain A: S.80, H.84, K.85 Chain B: L.58 Ligands: UMP.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.80, A:K.85 MPD.8: 5 residues within 4Å: Chain B: S.80, H.84, K.85 Chain C: L.58 Ligands: UMP.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.80, B:K.85

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

SO4.3: 2 residues within 4Å: Chain A: R.42, R.124 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.123 Salt bridges: A:R.42, A:R.124 SO4.6: 2 residues within 4Å: Chain B: R.42, R.124 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.123 Salt bridges: B:R.42, B:R.124 SO4.9: 2 residues within 4Å: Chain C: R.42, R.124 3 PLIP interactions: 3 interactions with chain C Water bridges: C:D.123 Salt bridges: C:R.42, C:R.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of Deoxyuridine 5'-triphosphate nucleotidohydrolase from Legionella pneumophila Philadelphia 1 in complex with dUMP (Deoxyuridine 5'-monophosphate). TO BE PUBLISHED

Release Date

2018-09-12

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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