SMTL ID : 6sqy.1

Mouse dCTPase in complex with dCMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.63, E.66, E.95, D.98 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.63, A:E.66, A:E.95, A:D.98, H2O.2, H2O.2 MG.3: 4 residues within 4Å: Chain B: E.63, E.66, E.95, D.98 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.63, B:E.66, B:E.95, B:D.98, H2O.4, H2O.5 MG.5: 4 residues within 4Å: Chain C: E.63, E.66, E.95, D.98 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.63, C:E.66, C:E.95, C:D.98, H2O.9, H2O.9 MG.7: 4 residues within 4Å: Chain D: E.63, E.66, E.95, D.98 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.63, D:E.66, D:E.95, D:D.98, H2O.11, H2O.12

4 x DCM: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DCM.2: 12 residues within 4Å: Chain A: H.38, F.41, W.47, H.51, E.63, D.98, I.101, Y.102 Chain B: W.73 Chain C: K.121, N.125, Y.129 9 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:W.47, B:W.73 Hydrogen bonds: A:H.51, A:Y.102, C:N.125 Water bridges: C:K.121, C:Y.129, B:Q.72 Salt bridges: C:K.121 DCM.4: 13 residues within 4Å: Chain A: W.73 Chain B: H.38, F.41, W.47, H.51, E.63, D.98, I.101, Y.102 Chain D: K.121, N.125, R.128, Y.129 15 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: B:W.47, B:Y.102, A:W.73 Hydrogen bonds: B:H.51, B:D.98, D:N.125, D:R.128, D:Y.129 Water bridges: B:E.63, B:E.63, B:Y.102, A:Q.72, D:K.121 Salt bridges: D:K.121, D:R.128 DCM.6: 12 residues within 4Å: Chain A: K.121, N.125, Y.129 Chain C: H.38, F.41, W.47, H.51, E.63, D.98, I.101, Y.102 Chain D: W.73 11 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: D:W.73, C:W.47 Water bridges: D:Q.72, C:Y.102, A:K.121, A:Y.129 Hydrogen bonds: C:H.51, C:D.98, A:N.125, A:Y.129 Salt bridges: A:K.121 DCM.8: 13 residues within 4Å: Chain B: K.121, N.125, R.128, Y.129 Chain C: W.73 Chain D: H.38, F.41, W.47, H.51, E.63, D.98, I.101, Y.102 14 PLIP interactions: 2 interactions with chain C, 7 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: C:W.73, D:W.47, D:Y.102 Water bridges: C:Q.72, D:E.63, D:E.63, D:Y.102, B:K.121 Hydrogen bonds: D:H.51, D:Y.102, B:N.125, B:R.128 Salt bridges: B:K.121, B:R.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scaletti, E. et al., The First Structure of an Active Mammalian dCTPase and its Complexes With Substrate Analogs and Products. J.Mol.Biol. (2020)

Release Date

2020-01-29

Peptides

dCTP pyrophosphatase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
A

D
D

dCTP pyrophosphatase 1

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