SMTL ID : 4a6a.2 (1 other biounit)

A115V variant of dCTP deaminase-dUTPase from Mycobacterium tuberculosis in complex with dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-hexamer

Ligands

6 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 22 residues within 4Å: Chain A: V.115, G.116, F.117, I.118, D.119, F.122, I.126, T.127, E.129, Y.162, G.168, S.169, K.170, Y.171, Q.174 Chain E: Q.28, K.101, S.102, S.103, R.106, Q.148 Ligands: MG.2 22 PLIP interactions: 13 interactions with chain A, 9 interactions with chain E Hydrophobic interactions: A:V.115, A:I.118, A:F.122 Hydrogen bonds: A:D.119, A:D.119, A:T.127, A:T.127, A:Y.162, A:K.170, A:Y.171, A:Q.174, E:Q.28, E:S.102, E:S.102, E:S.103, E:R.106, E:Q.148 Salt bridges: A:K.170, A:K.170, E:K.101, E:K.101 Water bridges: E:Q.28 TTP.3: 22 residues within 4Å: Chain B: V.115, G.116, F.117, I.118, D.119, F.122, I.126, T.127, E.129, Y.162, G.168, S.169, K.170, Y.171, Q.174 Chain D: Q.28, K.101, S.102, S.103, R.106, Q.148 Ligands: MG.4 21 PLIP interactions: 7 interactions with chain D, 14 interactions with chain B Hydrogen bonds: D:S.102, D:S.102, D:S.103, D:R.106, D:Q.148, B:D.119, B:D.119, B:D.119, B:T.127, B:T.127, B:Y.162, B:K.170, B:Q.174 Salt bridges: D:K.101, D:K.101, B:K.170, B:K.170 Hydrophobic interactions: B:V.115, B:I.118, B:I.118, B:F.122 TTP.6: 22 residues within 4Å: Chain A: Q.28, K.101, S.102, S.103, R.106, Q.148 Chain C: V.115, G.116, F.117, I.118, D.119, F.122, I.126, T.127, E.129, Y.162, G.168, S.169, K.170, Y.171, Q.174 Ligands: MG.7 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain C Hydrogen bonds: A:S.102, A:S.102, A:S.103, A:R.106, A:Q.148, C:D.119, C:D.119, C:T.127, C:T.127, C:K.170, C:Q.174 Salt bridges: A:K.101, A:K.101, C:K.170, C:K.170 Hydrophobic interactions: C:V.115, C:F.122 TTP.8: 22 residues within 4Å: Chain D: V.115, G.116, F.117, I.118, D.119, F.122, I.126, T.127, E.129, Y.162, G.168, S.169, K.170, Y.171, Q.174 Chain F: Q.28, K.101, S.102, S.103, R.106, Q.148 Ligands: MG.9 18 PLIP interactions: 7 interactions with chain F, 11 interactions with chain D Hydrogen bonds: F:S.102, F:S.102, F:S.103, F:R.106, F:Q.148, D:D.119, D:D.119, D:T.127, D:T.127, D:K.170, D:Q.174 Salt bridges: F:K.101, F:K.101, D:K.170, D:K.170 Hydrophobic interactions: D:V.115, D:I.118, D:F.122 TTP.10: 22 residues within 4Å: Chain C: Q.28, K.101, S.102, S.103, R.106, Q.148 Chain E: V.115, G.116, F.117, I.118, D.119, F.122, I.126, T.127, E.129, Y.162, G.168, S.169, K.170, Y.171, Q.174 Ligands: MG.11 20 PLIP interactions: 12 interactions with chain E, 8 interactions with chain C Hydrophobic interactions: E:V.115, E:F.122 Hydrogen bonds: E:D.119, E:D.119, E:D.119, E:T.127, E:T.127, E:Y.162, E:K.170, E:Q.174, C:Q.28, C:S.102, C:S.102, C:S.103, C:R.106, C:Q.148 Salt bridges: E:K.170, E:K.170, C:K.101, C:K.101 TTP.12: 22 residues within 4Å: Chain B: Q.28, K.101, S.102, S.103, R.106, Q.148 Chain F: V.115, G.116, F.117, I.118, D.119, F.122, I.126, T.127, E.129, Y.162, G.168, S.169, K.170, Y.171, Q.174 Ligands: MG.13 20 PLIP interactions: 8 interactions with chain B, 12 interactions with chain F Hydrogen bonds: B:Q.28, B:S.102, B:S.102, B:S.103, B:R.106, B:Q.148, F:D.119, F:D.119, F:T.127, F:T.127, F:K.170, F:Y.171, F:Q.174 Salt bridges: B:K.101, B:K.101, F:K.170, F:K.170 Hydrophobic interactions: F:V.115, F:I.118, F:F.122

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain E: Q.28, D.33, Q.148 Ligands: TTP.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain D: Q.28, D.33, Q.148 Ligands: TTP.3 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: E.99 Chain D: E.99 Chain F: E.99 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.99 MG.7: 4 residues within 4Å: Chain A: Q.28, D.33, Q.148 Ligands: TTP.6 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain F: Q.28, D.33, Q.148 Ligands: TTP.8 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: Q.28, D.33, Q.148 Ligands: TTP.10 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain B: Q.28, D.33 Ligands: TTP.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lovgreen, M.N. et al., Dttp Inhibition of the Bifunctional Dctp Deaminase- Dutpase from Mycobacterium Tuberculosis is Ph Dependent: Kinetic Analyses and Crystal Structure of A115V Variant. To be Published

Release Date

2012-10-10

Peptides

DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

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