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

Mycobacterium tuberculosis dUTPase complexed with magnesium and dUDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: DUD.6 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: D.48 Ligands: DUD.8 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: D.48, R.84 Ligands: DUD.2 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: DUD.14 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain E: D.48 Ligands: DUD.16 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain F: D.48, R.84 Ligands: DUD.10 No protein-ligand interaction detected (PLIP)

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

DUD.2: 14 residues within 4Å: Chain A: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Chain B: R.160 Chain C: R.84, S.85, G.86 Ligands: MG.7 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:S.85, C:G.86, A:N.97, A:D.103, A:K.111, A:K.111 Water bridges: C:P.83, A:T.101 Salt bridges: C:R.84 Hydrophobic interactions: A:Y.106 DUD.6: 15 residues within 4Å: Chain A: R.84, S.85, G.86, Q.133 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 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.102, B:Y.106 Hydrogen bonds: B:N.97, B:D.103, B:Y.106, B:K.111, B:K.111, A:S.85, A:G.86, A:Q.133 Water bridges: A:R.84, A:R.84 Salt bridges: A:R.84 DUD.8: 14 residues within 4Å: Chain B: R.84, S.85, G.86, Q.133 Chain C: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Ligands: MG.5 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.102, C:Y.106 Hydrogen bonds: C:N.97, C:D.103, C:K.111, C:K.111, B:S.85, B:G.86, B:Q.133 Salt bridges: B:R.84 DUD.10: 14 residues within 4Å: Chain D: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Chain E: R.160 Chain F: R.84, S.85, G.86 Ligands: MG.15 12 PLIP interactions: 3 interactions with chain F, 9 interactions with chain D Hydrogen bonds: F:S.85, F:G.86, D:N.97, D:D.103, D:D.103, D:Y.106, D:K.111, D:K.111 Salt bridges: F:R.84 Hydrophobic interactions: D:Y.106 Water bridges: D:T.101, D:T.101 DUD.14: 15 residues within 4Å: Chain D: R.84, S.85, G.86, Q.133 Chain E: V.81, N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Ligands: MG.9 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain E Hydrogen bonds: D:S.85, D:G.86, D:Q.133, E:N.97, E:D.103, E:D.103, E:K.111, E:K.111 Water bridges: D:R.84, D:R.84 Salt bridges: D:R.84 Hydrophobic interactions: E:I.102, E:Y.106 DUD.16: 14 residues within 4Å: Chain E: R.84, S.85, G.86, Q.133 Chain F: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Ligands: MG.13 12 PLIP interactions: 4 interactions with chain E, 8 interactions with chain F Hydrogen bonds: E:S.85, E:G.86, E:Q.133, F:N.97, F:D.103, F:D.103, F:Y.106, F:K.111, F:K.111 Salt bridges: E:R.84 Hydrophobic interactions: F:I.102, F:Y.106

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

TRS.3: 12 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, P.99, Q.137 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:H.82, C:Q.137, A:H.82, A:Q.137, B:H.82 TRS.4: 11 residues within 4Å: Chain A: S.94, I.95, V.96, S.98 Chain B: S.94, I.95, V.96, L.117 Chain C: S.94, I.95, V.96 7 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:S.94, C:V.96, A:S.94, A:S.94, A:V.96, A:S.98, B:S.94 TRS.11: 12 residues within 4Å: Chain D: L.80, H.82, P.99, Q.137 Chain E: L.80, H.82, P.99, Q.137 Chain F: L.80, H.82, P.99, Q.137 5 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: F:H.82, F:Q.137, D:H.82, D:Q.137, E:H.82 TRS.12: 11 residues within 4Å: Chain D: S.94, I.95, V.96, S.98 Chain E: S.94, I.95, V.96, L.117 Chain F: S.94, I.95, V.96 7 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E, 4 interactions with chain D Hydrogen bonds: F:S.94, F:V.96, E:S.94, D:S.94, D:S.94, D:V.96, D:S.98

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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