SMTL ID : 4p9d.1

Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in complex with dTMP and dTTP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.70, E.72, C.98, C.101 Ligands: TMP.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.70, A:C.98, A:C.101, H2O.1 ZN.6: 4 residues within 4Å: Chain B: H.70, C.98, C.101 Ligands: TMP.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.70, B:C.98, B:C.101, H2O.1 ZN.11: 5 residues within 4Å: Chain C: H.70, E.72, C.98, C.101 Ligands: TMP.14 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.70, C:C.98, C:C.101, H2O.1 ZN.15: 4 residues within 4Å: Chain D: H.70, C.98, C.101 Ligands: TMP.18 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.70, D:C.98, D:C.101, H2O.1 ZN.19: 5 residues within 4Å: Chain E: H.70, E.72, C.98, C.101 Ligands: TMP.22 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.70, E:C.98, E:C.101, H2O.2 ZN.24: 5 residues within 4Å: Chain F: H.70, E.72, C.98, C.101 Ligands: TMP.27 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.70, F:C.98, F:C.101, H2O.2

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: T.48, P.49, G.51, F.52, N.55 Ligands: TTP.3 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: P.49, N.55 Ligands: TTP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: P.49, N.55 Ligands: TTP.13 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain D: T.48, P.49, N.55 Ligands: TTP.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain E: P.49, N.55 Ligands: TTP.21 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain F: N.55 Ligands: TTP.26 No protein-ligand interaction detected (PLIP)

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

TTP.3: 15 residues within 4Å: Chain A: H.43, G.44, W.45, G.47, T.48, S.50, G.51, F.52, N.55, N.74, K.78 Chain B: K.5, G.38 Chain D: Q.107 Ligands: MG.2 15 PLIP interactions: 1 interactions with chain D, 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: D:Q.107, A:H.43, A:W.45, A:T.48, A:G.51, A:F.52, A:N.74, A:K.78 Water bridges: A:F.52, A:N.55 pi-Stacking: A:W.45 pi-Cation interactions: A:K.78 Salt bridges: B:K.5, B:K.5, B:K.5 TTP.9: 15 residues within 4Å: Chain A: K.5, G.38 Chain B: H.43, G.44, W.45, G.47, T.48, P.49, S.50, G.51, N.55, N.74, K.78 Chain C: Q.107 Ligands: MG.7 14 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A, 10 interactions with chain B Hydrogen bonds: C:Q.107, B:H.43, B:W.45, B:T.48, B:G.51, B:N.55, B:N.74 Salt bridges: A:K.5, A:K.5, A:K.5 Hydrophobic interactions: B:W.45 Water bridges: B:F.52, B:F.52 pi-Stacking: B:W.45 TTP.13: 11 residues within 4Å: Chain B: Q.107 Chain C: H.43, G.44, W.45, G.47, T.48, S.50, G.51, N.55, N.74 Ligands: MG.12 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:H.43, C:W.45, C:T.48, C:G.51, C:N.55, C:N.74, B:Q.107 Water bridges: C:H.43 pi-Stacking: C:W.45, C:W.45 TTP.17: 12 residues within 4Å: Chain A: Q.107 Chain D: H.43, G.44, W.45, G.47, T.48, S.50, G.51, N.55, N.74 Chain E: K.5 Ligands: MG.16 14 PLIP interactions: 10 interactions with chain D, 1 interactions with chain A, 3 interactions with chain E Hydrogen bonds: D:H.43, D:W.45, D:T.48, D:G.51, D:N.55, D:N.55, D:N.55, D:N.74, A:Q.107 pi-Stacking: D:W.45, D:W.45 Salt bridges: E:K.5, E:K.5, E:K.5 TTP.21: 14 residues within 4Å: Chain D: K.5 Chain E: H.43, G.44, W.45, G.47, T.48, P.49, S.50, G.51, N.55, N.74, K.78 Chain F: Q.107 Ligands: MG.20 15 PLIP interactions: 11 interactions with chain E, 3 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: E:W.45 Hydrogen bonds: E:H.43, E:W.45, E:T.48, E:P.49, E:G.51, E:N.55, E:N.55, E:N.74, F:Q.107 pi-Stacking: E:W.45, E:W.45 Salt bridges: D:K.5, D:K.5, D:K.5 TTP.26: 12 residues within 4Å: Chain C: K.5 Chain E: Q.107 Chain F: H.43, G.44, W.45, G.47, T.48, S.50, G.51, N.55, N.74 Ligands: MG.25 15 PLIP interactions: 11 interactions with chain F, 3 interactions with chain C, 1 interactions with chain E Hydrogen bonds: F:H.43, F:W.45, F:T.48, F:G.51, F:N.55, F:N.74, E:Q.107 Water bridges: F:H.43, F:F.52, F:F.52 pi-Stacking: F:W.45, F:W.45 Salt bridges: C:K.5, C:K.5, C:K.5

6 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.4: 13 residues within 4Å: Chain A: C.25, R.27, M.28, V.30, N.46, T.64, H.70, A.71, E.72, P.97, C.98, Y.119 Ligands: ZN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.119 Hydrogen bonds: A:N.46, A:A.71, A:E.72, A:C.98, A:Y.119 Salt bridges: A:R.27 pi-Stacking: A:H.70 TMP.8: 16 residues within 4Å: Chain B: C.25, R.27, M.28, V.30, N.46, T.64, V.68, H.70, A.71, E.72, S.96, P.97, C.98, Y.119, R.120 Ligands: ZN.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.119 Hydrogen bonds: B:N.46, B:A.71, B:E.72, B:C.98, B:Y.119, B:R.120 Salt bridges: B:R.27 pi-Stacking: B:H.70 TMP.14: 15 residues within 4Å: Chain C: C.25, R.27, M.28, V.30, N.46, T.64, V.68, H.70, A.71, E.72, S.96, P.97, C.98, Y.119 Ligands: ZN.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.119 Hydrogen bonds: C:N.46, C:A.71, C:E.72, C:C.98, C:Y.119 Salt bridges: C:R.27 pi-Stacking: C:H.70 TMP.18: 13 residues within 4Å: Chain D: C.25, R.27, M.28, V.30, N.46, T.64, H.70, A.71, E.72, C.98, Y.119, R.120 Ligands: ZN.15 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.119 Hydrogen bonds: D:N.46, D:T.64, D:A.71, D:E.72, D:C.98, D:R.120 Salt bridges: D:R.27 pi-Stacking: D:H.70 TMP.22: 14 residues within 4Å: Chain E: C.25, R.27, M.28, V.30, N.46, T.64, H.70, A.71, E.72, S.96, P.97, C.98, Y.119 Ligands: ZN.19 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:Y.119 Hydrogen bonds: E:N.46, E:T.64, E:A.71, E:E.72, E:C.98, E:Y.119 Salt bridges: E:R.27 pi-Stacking: E:H.70 TMP.27: 12 residues within 4Å: Chain F: R.27, M.28, V.30, N.46, T.64, H.70, A.71, E.72, P.97, C.98, Y.119 Ligands: ZN.24 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:Y.119 Hydrogen bonds: F:N.46, F:T.64, F:T.64, F:A.71, F:E.72, F:C.98, F:Y.119 Water bridges: F:R.27 Salt bridges: F:R.27 pi-Stacking: F:H.70

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 7 residues within 4Å: Chain A: M.79, A.80, S.82, E.84 Chain D: M.79, S.82, E.84 Ligand excluded by PLIP CL.10: 8 residues within 4Å: Chain B: M.79, A.80, S.82, E.84 Chain C: M.79, A.80, S.82, E.84 Ligand excluded by PLIP CL.23: 7 residues within 4Å: Chain E: M.79, S.82, S.83, E.84 Chain F: M.79, S.82, E.84 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marx, A. et al., The First Crystal Structure of a dTTP-bound Deoxycytidylate Deaminase Validates and Details the Allosteric-Inhibitor Binding Site. J.Biol.Chem. (2015)

Release Date

2014-11-26

Peptides

Deoxycytidylate deaminase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Deoxycytidylate deaminase

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