SMTL ID : 1xs1.3 (2 other biounits)

dCTP deaminase from Escherichia coli in complex with dUTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: DUT.4 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Ligands: DUT.6 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: DUT.2 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain D: D.34 Ligands: DUT.10 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: DUT.12 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: DUT.8 No protein-ligand interaction detected (PLIP)

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

DUT.2: 21 residues within 4Å: Chain A: L.107, A.124, H.125, R.126, I.127, D.128, W.131, I.135, V.136, Y.171, R.174, D.176, A.177, K.178, Y.179, Q.182 Chain C: R.110, S.111, S.112, R.115 Ligands: MG.5 28 PLIP interactions: 20 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:I.127, A:W.131 Hydrogen bonds: A:R.126, A:D.128, A:D.128, A:V.136, A:V.136, A:Y.171, A:K.178, A:Q.182, C:S.111, C:S.111, C:S.112, C:R.115 Water bridges: A:R.126, A:R.126, A:R.126, A:R.126, A:R.174, A:R.174, A:R.174, A:R.174, C:R.110, C:R.110 Salt bridges: A:R.126, A:R.174, C:R.110, C:R.110 DUT.4: 20 residues within 4Å: Chain A: R.110, S.111, S.112, R.115 Chain B: L.107, A.124, H.125, 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.1 31 PLIP interactions: 8 interactions with chain A, 23 interactions with chain B Hydrogen bonds: 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 Water bridges: A:R.110, A:R.110, B:R.126, B:R.126, B:R.126, B:R.126, B:R.126, B:R.174, B:R.174, B:R.174, B:R.174 Salt bridges: A:R.110, A:R.110, B:R.126, B:R.174, B:K.178, B:K.178 Hydrophobic interactions: B:I.127, B:W.131 DUT.6: 20 residues within 4Å: Chain B: R.110, S.111, S.112, R.115 Chain C: L.107, A.124, H.125, 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.3 28 PLIP interactions: 22 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:I.127, C:W.131 Hydrogen bonds: C:R.126, C:D.128, C:D.128, C:V.136, C:V.136, C:Y.171, C:K.178, C:Q.182, B:S.111, 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.126, C:R.126, C:R.126, C:K.178 Salt bridges: C:R.126, C:R.174, C:K.178, C:K.178, B:R.110, B:R.110 DUT.8: 19 residues within 4Å: Chain D: L.107, A.124, H.125, R.126, 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.11 23 PLIP interactions: 17 interactions with chain D, 6 interactions with chain F Hydrophobic interactions: D:W.131 Hydrogen bonds: D:R.126, D:D.128, D:V.136, D:V.136, D:K.178, D:Q.182, F:R.110, F:S.111, F:S.111, F:S.112, F:R.115 Water bridges: D:R.126, D:R.126, D:R.126, D:R.126, D:R.126, D:R.174 Salt bridges: D:R.126, D:R.174, D:K.178, D:K.178, F:R.110 DUT.10: 20 residues within 4Å: Chain D: R.110, S.111, S.112, R.115 Chain E: A.124, H.125, R.126, I.127, D.128, W.131, I.135, V.136, Y.171, R.174, D.176, A.177, K.178, Y.179, Q.182 Ligands: MG.7 25 PLIP interactions: 8 interactions with chain D, 17 interactions with chain E Hydrogen bonds: D:S.111, D:S.111, D:S.112, D:R.115, E:R.126, E:D.128, E:V.136, E:V.136, E:K.178, E:Q.182 Water bridges: D:R.110, D:R.110, E:R.126, E:R.126, E:R.126, E:R.126, E:R.126, E:R.126 Salt bridges: D:R.110, D:R.110, E:R.126, E:R.174, E:K.178 Hydrophobic interactions: E:I.127, E:W.131 DUT.12: 20 residues within 4Å: Chain E: R.110, S.111, S.112, R.115 Chain F: L.107, A.124, H.125, 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.9 31 PLIP interactions: 8 interactions with chain E, 23 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 Water bridges: E:R.110, E:R.110, F:R.126, F:R.126, F:R.126, F:R.126, F:R.126, F:R.126, F:R.126, F:R.174, F:R.174, F:K.178 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, E. et al., Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes. J.Biol.Chem. (2005)

Release Date

2004-12-21

Peptides

Deoxycytidine triphosphate deaminase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Deoxycytidine triphosphate deaminase

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