SMTL ID : 6sqw.1

Mouse dCTPase in complex with 5-Me-dCMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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.6 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.8, 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.13

4 x 5CM: 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

5CM.2: 12 residues within 4Å: Chain A: H.38, F.41, W.47, H.51, D.98, I.101, Y.102 Chain B: W.73 Chain C: K.121, N.125, R.128, Y.129 18 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: B:W.73, A:W.47, A:W.47, A:Y.102, C:Y.129 Water bridges: B:Q.72, A:E.66, A:D.98, A:D.98, C:K.121, C:K.121 Hydrogen bonds: A:H.51, A:Y.102, C:N.125, C:R.128, C:Y.129 Salt bridges: C:K.121, C:R.128 5CM.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 19 PLIP interactions: 7 interactions with chain D, 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: D:Y.129, B:W.47, B:W.47, B:I.101, B:Y.102, A:W.73 Hydrogen bonds: D:N.125, D:R.128, D:Y.129, D:Y.129, B:H.51, B:D.98 Salt bridges: D:K.121, D:R.128 Water bridges: B:E.63, B:E.63, B:E.66, B:D.98, B:Y.102 5CM.6: 12 residues within 4Å: Chain A: K.121, N.125, R.128, Y.129 Chain C: H.38, F.41, W.47, H.51, D.98, I.101, Y.102 Chain D: W.73 19 PLIP interactions: 9 interactions with chain A, 9 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:Y.129, C:W.47, C:W.47, C:Y.102, D:W.73 Hydrogen bonds: A:N.125, A:R.128, A:Y.129, A:Y.129, C:H.51, C:D.98 Water bridges: A:K.121, A:K.121, C:E.66, C:D.98, C:D.98, C:Y.102 Salt bridges: A:K.121, A:R.128 5CM.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 16 PLIP interactions: 9 interactions with chain D, 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: D:W.47, D:W.47, D:I.101, D:Y.102, B:Y.129, C:W.73 Hydrogen bonds: D:H.51, D:Y.102, B:N.125, B:R.128, B:Y.129 Water bridges: D:E.63, D:E.66, D:D.98 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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