SMTL ID : 2v9x.2 (1 other biounit)

E138D variant of Escherichia coli dCTP deaminase in complex with dUTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x DUT: DEOXYURIDINE-5'-TRIPHOSPHATE(Non-covalent)

DUT.1: 18 residues within 4Å: Chain A: A.124, R.126, I.127, D.128, W.131, I.135, V.136, Y.171, R.174, A.177, K.178, Y.179, Q.182 Chain C: R.110, S.111, S.112, R.115 Ligands: MG.2 24 PLIP interactions: 6 interactions with chain C, 18 interactions with chain A Hydrogen bonds: C:S.111, C:S.111, C:S.112, C:R.115, A:R.126, A:D.128, A:D.128, A:V.136, A:V.136, A:K.178, A:Q.182 Salt bridges: C:R.110, C:R.110, A:R.126, A:R.174, A:K.178, A:K.178 Hydrophobic interactions: A:W.131 Water bridges: A:R.126, A:R.126, A:R.126, A:R.126, A:R.126, A:R.126 DUT.4: 19 residues within 4Å: Chain A: G.109, R.110, S.111, S.112, R.115 Chain B: A.124, R.126, I.127, D.128, W.131, I.135, V.136, Y.171, R.174, A.177, K.178, Y.179, Q.182 Ligands: MG.5 25 PLIP interactions: 6 interactions with chain A, 19 interactions with chain B Hydrogen bonds: A:R.110, A:S.111, A:S.111, A:S.112, A:R.115, B:R.126, B:D.128, B:D.128, B:V.136, B:V.136, B:Y.171, B:K.178, B:Q.182 Salt bridges: A:R.110, B:R.126, B:R.174, B:K.178, B:K.178 Hydrophobic interactions: B:I.127, B:W.131 Water bridges: B:R.126, B:R.126, B:R.174, B:R.174, B:R.174 DUT.6: 17 residues within 4Å: Chain B: R.110, S.111, S.112, R.115 Chain C: A.124, R.126, D.128, W.131, I.135, V.136, Y.171, R.174, A.177, K.178, Y.179, Q.182 Ligands: MG.7 23 PLIP interactions: 18 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:W.131 Hydrogen bonds: C:R.126, C:D.128, C:D.128, C:V.136, C:V.136, C:K.178, C:Q.182, B:R.110, B:S.111, B:S.112, B:R.115 Water bridges: C:R.126, C:R.126, C:R.126, C:R.126, C:R.174, C:R.174 Salt bridges: C:R.126, C:R.174, C:K.178, C:K.178, B:R.110 DUT.8: 18 residues within 4Å: Chain D: A.124, R.126, I.127, D.128, W.131, I.135, V.136, Y.171, R.174, A.177, K.178, Y.179, Q.182 Chain F: R.110, S.111, S.112, R.115 Ligands: MG.9 22 PLIP interactions: 6 interactions with chain F, 16 interactions with chain D Hydrogen bonds: F:R.110, F:S.111, F:S.111, F:S.112, F:R.115, D:R.126, D:D.128, D:V.136, D:V.136, D:K.178, D:Q.182 Salt bridges: F:R.110, D:R.126, D:R.174, D:K.178, D:K.178 Hydrophobic interactions: D:I.127, D:W.131 Water bridges: D:R.126, D:R.126, D:R.126, D:R.126 DUT.11: 18 residues within 4Å: Chain D: R.110, S.111, S.112, R.115 Chain E: A.124, R.126, I.127, D.128, W.131, I.135, V.136, Y.171, R.174, A.177, K.178, Y.179, Q.182 Ligands: MG.12 26 PLIP interactions: 18 interactions with chain E, 8 interactions with chain D Hydrophobic interactions: E:W.131 Hydrogen bonds: E:R.126, E:D.128, E:V.136, E:V.136, E:Y.171, E:K.178, E:Q.182, D:S.111, D:S.111, D:S.112, D:R.115 Water bridges: E:R.126, E:R.126, E:R.126, E:R.126, E:R.174, E:R.174, D:R.110, D:R.110 Salt bridges: E:R.126, E:R.174, E:K.178, E:K.178, D:R.110, D:R.110 DUT.13: 18 residues within 4Å: Chain E: R.110, S.111, S.112, R.115 Chain F: A.124, R.126, I.127, D.128, W.131, I.135, V.136, Y.171, R.174, A.177, K.178, Y.179, Q.182 Ligands: MG.14 25 PLIP interactions: 6 interactions with chain E, 19 interactions with chain F Hydrogen bonds: E:S.111, E:S.111, E:S.112, E:R.115, F:R.126, F:D.128, F:V.136, F:V.136, F:Y.171, F:K.178, F:Q.182 Salt bridges: E:R.110, E:R.110, F:R.126, F:R.174, F:K.178, F:K.178 Hydrophobic interactions: F:I.127, F:W.131 Water bridges: F:R.126, F:R.126, F:R.126, F:R.126, F:R.126, F:R.126

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

MG.2: 1 residues within 4Å: Ligands: DUT.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: DUT.4 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: DUT.6 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: DUT.8 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: DUT.11 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: DUT.13 No protein-ligand interaction detected (PLIP)

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

SO4.3: 6 residues within 4Å: Chain A: R.2, H.125 Chain B: R.2, H.125 Chain C: R.2, H.125 8 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B, 2 interactions with chain C Water bridges: A:H.125, B:H.125 Salt bridges: A:R.2, A:H.125, B:R.2, B:H.125, C:R.2, C:H.125 SO4.10: 6 residues within 4Å: Chain D: R.2, H.125 Chain E: R.2, H.125 Chain F: R.2, H.125 8 PLIP interactions: 4 interactions with chain D, 2 interactions with chain F, 2 interactions with chain E Water bridges: D:R.2, D:S.159 Salt bridges: D:R.2, D:H.125, F:R.2, F:H.125, E:R.2, E:H.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thymark, M. et al., Mutational Analysis of the Nucleotide Binding Site of Escherichia Coli Dctp Deaminase. Arch.Biochem.Biophys. (2008)

Release Date

2007-11-20

Peptides

DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
G

E
H

F
I

DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

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