SMTL ID : 2yzj.1

Crystal structure of dCTP deaminase from Sulfolobus tokodaii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-trimer

Ligands

3 x DUD: DEOXYURIDINE-5'-DIPHOSPHATE(Non-covalent)

DUD.1: 14 residues within 4Å: Chain A: I.99, T.115, V.116, I.117, D.118, Y.121, V.125, N.126, Y.159, Y.163 Chain B: K.102, S.103, T.104, R.107 25 PLIP interactions: 15 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:S.103, B:S.103, B:S.103, B:T.104, B:T.104, B:R.107, B:R.107, A:D.118, A:D.118, A:D.118, A:N.126, A:N.126, A:Y.159 Water bridges: B:R.35, B:R.35, B:D.40, B:K.102, B:K.102, B:K.102, A:N.126 Salt bridges: B:K.102, B:K.102 Hydrophobic interactions: A:I.99, A:I.117, A:Y.121 DUD.6: 14 residues within 4Å: Chain B: I.99, T.115, V.116, I.117, D.118, Y.121, V.125, N.126, Y.159, Y.163 Chain C: K.102, S.103, T.104, R.107 22 PLIP interactions: 10 interactions with chain B, 12 interactions with chain C Hydrophobic interactions: B:I.99, B:I.117, B:Y.121 Hydrogen bonds: B:D.118, B:D.118, B:D.118, B:N.126, B:N.126, B:Y.159, C:S.103, C:S.103, C:S.103, C:T.104, C:R.107, C:R.107 Water bridges: B:N.126, C:D.40, C:D.40, C:K.102, C:K.102 Salt bridges: C:K.102, C:K.102 DUD.7: 14 residues within 4Å: Chain A: K.102, S.103, T.104, R.107 Chain C: I.99, T.115, V.116, I.117, D.118, Y.121, V.125, N.126, Y.159, Y.163 23 PLIP interactions: 9 interactions with chain C, 14 interactions with chain A Hydrophobic interactions: C:I.99, C:I.117, C:Y.121 Hydrogen bonds: C:D.118, C:D.118, C:D.118, C:N.126, C:N.126, A:S.103, A:S.103, A:S.103, A:T.104, A:T.104, A:R.107, A:R.107 Water bridges: C:N.126, A:R.35, A:R.35, A:D.40, A:K.102, A:K.102 Salt bridges: A:K.102, A:K.102

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 8 residues within 4Å: Chain A: N.78, V.132 Chain B: N.78, T.130, V.132 Chain C: N.78, T.130, V.132 8 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: A:N.78, B:N.78, C:N.78 Water bridges: A:N.78, A:N.78, B:N.78, C:N.78, C:N.78

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: P.114 Chain B: P.114 Chain C: L.98, P.114 Ligands: MG.4, MG.5 No protein-ligand interaction detected (PLIP) MG.4: 7 residues within 4Å: Chain A: P.114 Chain B: L.98, I.99, T.100, P.114 Ligands: MG.3, MG.5 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: P.114 Chain B: P.114 Chain C: P.114 Ligands: MG.3, MG.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanagawa, M. et al., Crystal structure of dCTP deaminase from Sulfolobus tokodaii. To be Published

Release Date

2007-11-06

Peptides

167aa long hypothetical dUTPase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

167aa long hypothetical dUTPase

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