SMTL ID : 4p9c.2 (1 other biounit)

Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in complex with dCMP and dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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: DU.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.70, A:C.98, A:C.101, H2O.2 ZN.4: 5 residues within 4Å: Chain B: H.70, E.72, C.98, C.101 Ligands: DU.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.70, B:C.98, B:C.101 ZN.7: 5 residues within 4Å: Chain C: H.70, E.72, C.98, C.101 Ligands: DU.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.70, C:C.98, C:C.101 ZN.10: 5 residues within 4Å: Chain D: H.70, E.72, C.98, C.101 Ligands: DU.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.70, D:C.98, D:C.101, H2O.5 ZN.13: 5 residues within 4Å: Chain E: H.70, E.72, C.98, C.101 Ligands: DU.15 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.70, E:C.98, E:C.101, H2O.6 ZN.16: 5 residues within 4Å: Chain F: H.70, E.72, C.98, C.101 Ligands: DU.18 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.70, F:C.98, F:C.101, H2O.7

6 x DCM: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DCM.2: 11 residues within 4Å: Chain A: H.43, G.44, W.45, G.47, T.48, P.49, S.50, N.74, K.78 Chain D: Q.107 Chain E: K.5 8 PLIP interactions: 6 interactions with chain A, 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: A:H.43, A:W.45, A:W.45, A:N.74, A:K.78, D:Q.107 pi-Stacking: A:W.45 Salt bridges: E:K.5 DCM.5: 12 residues within 4Å: Chain B: H.43, G.44, W.45, G.47, T.48, S.50, G.51, N.74, K.78 Chain E: Q.107 Chain F: K.5, G.38 10 PLIP interactions: 8 interactions with chain B, 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: B:H.43, B:W.45, B:G.47, B:G.51, B:N.74, E:Q.107 Water bridges: B:T.48, B:N.55 pi-Stacking: B:W.45 Salt bridges: F:K.5 DCM.8: 8 residues within 4Å: Chain C: H.43, G.44, W.45, G.47, T.48, S.50, N.74 Chain F: Q.107 10 PLIP interactions: 1 interactions with chain D, 8 interactions with chain C, 1 interactions with chain F Salt bridges: D:K.5 Hydrogen bonds: C:H.43, C:W.45, C:W.45, C:S.50, C:N.74, F:Q.107 Water bridges: C:G.51, C:G.51 pi-Stacking: C:W.45 DCM.11: 8 residues within 4Å: Chain A: Q.107 Chain D: H.43, G.44, W.45, G.47, T.48, S.50, N.74 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.43, D:W.45, D:G.47, D:S.50, D:N.74, A:Q.107 Water bridges: D:H.43 pi-Stacking: D:W.45 DCM.14: 9 residues within 4Å: Chain A: G.38 Chain B: Q.107 Chain E: H.43, G.44, W.45, G.47, T.48, S.50, N.74 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:Q.107, E:H.43, E:W.45, E:N.74 pi-Stacking: E:W.45 DCM.17: 10 residues within 4Å: Chain B: G.38 Chain C: Q.107 Chain F: H.43, G.44, W.45, G.47, T.48, S.50, N.74, K.78 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:H.43, F:W.45, F:G.47, F:N.74, C:Q.107 pi-Stacking: F:W.45

6 x DU: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

DU.3: 13 residues within 4Å: Chain A: 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.1 Protein-ligand interaction information (PLIP) not available DU.6: 13 residues within 4Å: Chain B: C.25, R.27, V.30, N.46, T.64, H.70, A.71, E.72, P.97, C.98, Y.119, R.120 Ligands: ZN.4 Protein-ligand interaction information (PLIP) not available DU.9: 13 residues within 4Å: Chain C: 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.7 Protein-ligand interaction information (PLIP) not available DU.12: 15 residues within 4Å: Chain D: 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, R.120 Ligands: ZN.10 Protein-ligand interaction information (PLIP) not available DU.15: 13 residues within 4Å: Chain E: 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.13 Protein-ligand interaction information (PLIP) not available DU.18: 14 residues within 4Å: Chain F: C.25, R.27, V.30, N.46, T.64, H.70, A.71, E.72, S.96, P.97, C.98, Y.119, R.120 Ligands: ZN.16 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:N.46, F:T.64, F:T.64, F:A.71, F:E.72, F:C.98 Water bridges: F:R.27, F:R.27 Salt bridges: F:R.27, F:R.120 pi-Stacking: F:H.70, F:Y.119

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
B

B
C

C
D

D
G

E
H

F
I

Deoxycytidylate deaminase

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