SMTL ID : 6sqz.1

Mouse dCTPase in complex with dCMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: E.63, E.66, E.95, D.98 Ligands: MG.2, 0KX.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.63, A:E.66, A:E.95, A:D.98, H2O.1 MG.2: 4 residues within 4Å: Chain A: E.63, E.66 Ligands: MG.1, 0KX.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.63, A:E.66, H2O.2 MG.4: 6 residues within 4Å: Chain B: E.63, E.66, E.95, D.98 Ligands: MG.5, 0KX.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.63, B:E.66, B:E.95, B:D.98, H2O.5 MG.5: 4 residues within 4Å: Chain B: E.63, E.66 Ligands: MG.4, 0KX.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.63, B:E.66, H2O.1 MG.7: 6 residues within 4Å: Chain C: E.63, E.66, E.95, D.98 Ligands: MG.8, 0KX.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.63, C:E.66, C:E.95, C:D.98, H2O.7 MG.8: 4 residues within 4Å: Chain C: E.63, E.66 Ligands: MG.7, 0KX.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.63, C:E.66, H2O.8 MG.10: 6 residues within 4Å: Chain D: E.63, E.66, E.95, D.98 Ligands: MG.11, 0KX.12 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.63, D:E.66, D:E.95, D:D.98, H2O.10 MG.11: 4 residues within 4Å: Chain D: E.63, E.66 Ligands: MG.10, 0KX.12 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.63, D:E.66, H2O.7

4 x 0KX: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine(Non-covalent)

0KX.3: 16 residues within 4Å: Chain A: H.38, F.41, W.47, H.51, E.63, E.66, D.98, I.101, Y.102 Chain B: W.73 Chain C: K.121, N.125, R.128, Y.129 Ligands: MG.1, MG.2 14 PLIP interactions: 8 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:D.98, A:Y.102, C:K.121, C:N.125, C:Y.129 Water bridges: A:E.66, A:E.66, A:D.98, A:D.98, B:Q.72 Salt bridges: C:R.128 0KX.6: 17 residues within 4Å: Chain A: E.69, W.73 Chain B: H.38, F.41, W.47, H.51, E.63, E.66, D.98, I.101, Y.102 Chain D: K.121, N.125, R.128, Y.129 Ligands: MG.4, MG.5 15 PLIP interactions: 7 interactions with chain D, 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:K.121, D:N.125, D:R.128, D:Y.129, B:H.51, B:D.98, B:D.98, B:Y.102 Water bridges: D:K.121, B:E.66, A:E.69 Salt bridges: D:R.128 pi-Stacking: D:Y.129 Hydrophobic interactions: B:W.47, B:Y.102 0KX.9: 16 residues within 4Å: Chain A: K.121, N.125, R.128, Y.129 Chain C: H.38, F.41, W.47, H.51, E.63, E.66, D.98, I.101, Y.102 Chain D: W.73 Ligands: MG.7, MG.8 18 PLIP interactions: 5 interactions with chain A, 8 interactions with chain C, 5 interactions with chain D Hydrogen bonds: A:K.121, A:N.125, A:Y.129, A:Y.129, C:H.51, C:D.98, C:D.98, C:Y.102 Salt bridges: A:R.128 Hydrophobic interactions: C:W.47, D:W.73 Water bridges: C:E.66, C:E.66, C:D.98, D:E.69, D:Q.72, D:Q.72, D:Q.72 0KX.12: 17 residues within 4Å: Chain B: K.121, N.125, R.128, Y.129 Chain C: E.69, W.73 Chain D: H.38, F.41, W.47, H.51, E.63, E.66, D.98, I.101, Y.102 Ligands: MG.10, MG.11 14 PLIP interactions: 7 interactions with chain D, 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: D:W.47, D:Y.102 Hydrogen bonds: D:H.51, D:D.98, D:Y.102, B:K.121, B:N.125, B:R.128 Water bridges: D:D.98, D:D.98, B:K.121, C:Q.72 Salt bridges: B:R.128 pi-Stacking: B:Y.129

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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