SMTL ID : 1snf.1

MYCOBACTERIUM TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND DEOXYURIDINE 5'-MONOPHOSPHATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: UMP.6 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: UMP.11 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: UMP.3 No protein-ligand interaction detected (PLIP)

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 7 residues within 4Å: Chain A: V.142, E.143, L.144 Chain C: P.37, S.38, R.39, V.47 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:P.37, C:R.39, A:L.144 Water bridges: C:R.39, C:R.39 NO3.5: 4 residues within 4Å: Chain B: R.84, G.86, L.87, R.90 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.84, B:L.87, B:R.90 Water bridges: B:G.86 NO3.10: 4 residues within 4Å: Chain A: F.150, D.151 Chain C: A.72, R.107 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.151, C:R.107, C:R.107

3 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.3: 13 residues within 4Å: Chain A: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Chain C: R.84, S.85, Q.133 Ligands: MG.9 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:Y.106 Hydrogen bonds: A:N.97, A:T.101, A:D.103, A:D.103, A:D.103, A:Y.106, A:K.111, A:K.111, C:S.85, C:S.85, C:S.85, C:Q.133 Water bridges: A:T.101, C:R.84 UMP.6: 13 residues within 4Å: Chain A: R.84, S.85 Chain B: V.81, N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Ligands: MG.1 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:S.85, A:S.85, A:G.86, B:N.97, B:T.101, B:D.103, B:D.103, B:K.111, B:K.111 Water bridges: A:R.84, A:Q.133, B:A.113, B:A.113 Hydrophobic interactions: B:Y.106 UMP.11: 14 residues within 4Å: Chain B: S.85, G.86, Q.133 Chain C: V.81, N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Ligands: MG.4 16 PLIP interactions: 8 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:Y.106 Hydrogen bonds: C:N.97, C:T.101, C:D.103, C:D.103, C:Y.106, C:K.111, C:K.111, B:S.85, B:S.85, B:S.85, B:G.86, B:Q.133 Water bridges: B:R.84, B:R.84, B:R.84

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

TRS.7: 11 residues within 4Å: Chain A: S.94, I.95, V.96, L.117 Chain B: S.94, I.95, V.96 Chain C: S.94, I.95, V.96, L.117 10 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:S.94, B:I.95, A:S.94, A:I.95, C:S.94, C:I.95 Water bridges: A:S.94, A:I.95, A:S.98, C:S.94 TRS.8: 11 residues within 4Å: Chain A: L.80, H.82, P.99, Q.137 Chain B: L.80, H.82, P.99, Q.137 Chain C: L.80, H.82, Q.137 7 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: A:H.82, A:Q.137, C:H.82, C:Q.137, B:H.82, B:Q.137, B:Q.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, S. et al., Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism. J.Mol.Biol. (2004)

Release Date

2004-03-16

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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