SMTL ID : 1smc.1

Mycobacterium tuberculosis dUTPase complexed with dUTP in the absence of metal ion.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

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

DUT.1: 14 residues within 4Å: Chain A: P.83, R.84, S.85, G.86, Q.133 Chain B: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:S.85, A:S.85, A:G.86, A:Q.133, B:N.97, B:T.101, B:D.103, B:D.103, B:K.111, B:K.111 Water bridges: A:R.84, A:L.87, A:Q.133, B:T.101, B:A.113, B:A.113 Salt bridges: A:R.84 Hydrophobic interactions: B:Y.106 DUT.5: 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, Q.133 23 PLIP interactions: 9 interactions with chain C, 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:R.84, C:S.85, C:S.85, C:G.86, C:Q.133, A:N.97, A:D.103, A:Y.106, A:K.111, A:K.111 Water bridges: C:R.84, C:L.87, C:Q.133, A:T.101, A:T.101, A:A.113, A:A.113, B:R.160, B:R.160 Salt bridges: C:R.84, B:R.160 Hydrophobic interactions: A:I.102, A:Y.106 DUT.6: 15 residues within 4Å: Chain B: D.48, R.84, 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 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:P.83, B:S.85, B:S.85, B:S.85, B:G.86, B:L.87, B:Q.133, C:N.97, C:T.101, C:D.103, C:D.103, C:K.111, C:K.111 Salt bridges: B:R.84, B:R.84 Hydrophobic interactions: C:Y.106 Water bridges: C:T.101

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

TRS.2: 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 7 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: B:H.82, B:Q.137, A:H.82, A:Q.137, A:Q.137, C:H.82, C:Q.137 TRS.3: 8 residues within 4Å: Chain A: G.60, N.116, L.117 Chain B: N.116, L.117 Chain C: G.60, N.116, L.117 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:N.116, B:N.116, C:N.116 Water bridges: A:L.117 TRS.7: 10 residues within 4Å: Chain A: S.94, I.95, V.96 Chain B: S.94, I.95, V.96 Chain C: S.94, I.95, V.96, L.117 11 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:S.94, A:I.95, C:S.94, C:I.95, B:S.94, B:I.95 Water bridges: A:S.94, A:S.98, A:S.98, C:S.94, C:S.98

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

NO3.4: 3 residues within 4Å: Chain A: F.150, D.151 Chain C: R.107 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.107, C:R.107, A:D.151

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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