SMTL ID : 2hvw.1

Crystal structure of dCMP deaminase from Streptococcus mutans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.58, C.88, H.93, C.100 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.58, A:C.88, A:H.93, A:C.100 ZN.2: 5 residues within 4Å: Chain A: H.105, E.107, C.133, C.136 Ligands: DDN.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.105, A:C.133, A:C.136 ZN.7: 4 residues within 4Å: Chain B: C.58, C.88, H.93, C.100 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.58, B:C.88, B:H.93, B:C.100 ZN.8: 5 residues within 4Å: Chain B: H.105, E.107, C.133, C.136 Ligands: DDN.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.105, B:C.133, B:C.136 ZN.13: 4 residues within 4Å: Chain C: C.58, C.88, H.93, C.100 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.58, C:C.88, C:H.93, C:C.100 ZN.14: 5 residues within 4Å: Chain C: H.105, E.107, C.133, C.136 Ligands: DDN.17 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.105, C:C.133, C:C.136 ZN.19: 4 residues within 4Å: Chain D: C.58, C.88, H.93, C.100 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.58, D:C.88, D:H.93, D:C.100 ZN.20: 5 residues within 4Å: Chain D: H.105, E.107, C.133, C.136 Ligands: DDN.23 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.105, D:C.133, D:C.136 ZN.25: 4 residues within 4Å: Chain E: C.58, C.88, H.93, C.100 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.58, E:C.88, E:H.93, E:C.100 ZN.26: 5 residues within 4Å: Chain E: H.105, E.107, C.133, C.136 Ligands: DDN.29 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.105, E:C.133, E:C.136 ZN.31: 4 residues within 4Å: Chain F: C.58, C.88, H.93, C.100 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.58, F:C.88, F:H.93, F:C.100 ZN.32: 5 residues within 4Å: Chain F: H.105, E.107, C.133, C.136 Ligands: DDN.35 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.105, F:C.133, F:C.136

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

MG.3: 1 residues within 4Å: Ligands: DCP.4 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: DCP.10 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: DCP.16 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Ligands: DCP.22 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Ligands: DCP.28 No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Ligands: DCP.34 No protein-ligand interaction detected (PLIP)

6 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.4: 16 residues within 4Å: Chain A: R.55, T.57, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109 Chain B: Q.142 Chain D: R.38, W.41, N.71, R.72 Ligands: MG.3 22 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B, 10 interactions with chain D Hydrophobic interactions: A:Y.78, D:W.41 Hydrogen bonds: A:Y.78, A:G.80, A:D.84, A:N.87, A:N.109, B:Q.142, D:N.71 Water bridges: A:R.55, A:T.85, D:R.38, D:R.38, D:Y.44, D:N.71, D:R.72, D:I.73 Salt bridges: A:R.55, A:R.55, D:R.38 pi-Stacking: A:Y.78 pi-Cation interactions: D:R.72 DCP.10: 16 residues within 4Å: Chain A: Q.142 Chain B: R.55, T.57, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109 Chain C: R.38, W.41, N.71, R.72 Ligands: MG.9 24 PLIP interactions: 16 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:Y.78, C:W.41 Hydrogen bonds: B:Y.78, B:G.80, B:G.80, B:D.84, B:N.109, C:N.71 Water bridges: B:R.55, B:T.76, B:D.84, B:T.85, B:N.87, B:N.87, B:N.87, C:R.38, C:R.38, C:Y.44, C:I.73 Salt bridges: B:R.55, B:R.55, C:R.38 pi-Stacking: B:Y.78 pi-Cation interactions: C:R.72 DCP.16: 16 residues within 4Å: Chain B: R.38, W.41, N.71, R.72 Chain C: R.55, T.57, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109 Chain F: Q.142 Ligands: MG.15 27 PLIP interactions: 8 interactions with chain B, 18 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: B:W.41, C:Y.78 Hydrogen bonds: B:N.71, C:Y.78, C:Y.78, C:G.80, C:G.80, C:D.84, C:N.109, F:Q.142 Water bridges: B:R.38, B:R.38, B:Y.44, B:I.73, C:R.55, C:T.76, C:T.85, C:N.87, C:N.87, C:N.87, C:N.87, C:N.87 Salt bridges: B:R.38, C:R.55, C:R.55 pi-Cation interactions: B:R.72 pi-Stacking: C:Y.78 DCP.22: 16 residues within 4Å: Chain A: R.38, W.41, N.71, R.72 Chain D: R.55, T.57, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109 Chain E: Q.142 Ligands: MG.21 24 PLIP interactions: 14 interactions with chain D, 1 interactions with chain E, 9 interactions with chain A Hydrophobic interactions: D:Y.78, A:W.41 Hydrogen bonds: D:Y.78, D:Y.78, D:G.80, D:D.84, D:N.87, D:N.109, E:Q.142, A:N.71 Water bridges: D:R.55, D:T.76, D:T.76, D:T.85, A:R.38, A:R.38, A:N.71, A:R.72, A:I.73 Salt bridges: D:R.55, D:R.55, A:R.38 pi-Stacking: D:Y.78 pi-Cation interactions: A:R.72 DCP.28: 16 residues within 4Å: Chain D: Q.142 Chain E: R.55, T.57, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109 Chain F: R.38, W.41, N.71, R.72 Ligands: MG.27 24 PLIP interactions: 17 interactions with chain E, 7 interactions with chain F Hydrophobic interactions: E:Y.78, F:W.41 Hydrogen bonds: E:Y.78, E:Y.78, E:G.80, E:G.80, E:D.84, E:N.109, F:N.71 Water bridges: E:R.55, E:D.84, E:D.84, E:T.85, E:N.87, E:N.87, E:N.87, F:R.38, F:R.38, F:I.73 Salt bridges: E:R.55, E:R.55, F:R.38 pi-Stacking: E:Y.78 pi-Cation interactions: F:R.72 DCP.34: 16 residues within 4Å: Chain C: Q.142 Chain E: R.38, W.41, N.71, R.72 Chain F: R.55, T.57, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109 Ligands: MG.33 24 PLIP interactions: 1 interactions with chain C, 7 interactions with chain E, 16 interactions with chain F Hydrogen bonds: C:Q.142, E:N.71, F:Y.78, F:G.80, F:G.80, F:D.84, F:N.109 Hydrophobic interactions: E:W.41, F:Y.78 Water bridges: E:R.38, E:R.38, E:I.73, F:R.55, F:T.85, F:N.87, F:N.87, F:N.87, F:N.87, F:N.87 Salt bridges: E:R.38, F:R.55, F:R.55 pi-Cation interactions: E:R.72 pi-Stacking: F:Y.78

6 x DDN: 3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

DDN.5: 17 residues within 4Å: Chain A: C.58, R.60, A.61, V.63, N.79, H.99, C.100, T.103, H.105, A.106, E.107, P.132, C.133, C.136, Y.154, R.155 Ligands: ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.79, A:C.100, A:T.103, A:A.106, A:C.133 Salt bridges: A:R.60, A:H.99, A:R.155 pi-Stacking: A:H.105 DDN.11: 18 residues within 4Å: Chain B: C.58, R.60, A.61, V.63, N.79, H.99, C.100, T.103, H.105, A.106, E.107, F.131, P.132, C.133, C.136, Y.154, R.155 Ligands: ZN.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.79, B:C.100, B:A.106, B:C.133, B:Y.154 Salt bridges: B:R.60, B:H.99, B:R.155 pi-Stacking: B:H.105 DDN.17: 17 residues within 4Å: Chain C: C.58, R.60, A.61, V.63, N.79, H.99, C.100, T.103, H.105, A.106, E.107, P.132, C.133, C.136, Y.154, R.155 Ligands: ZN.14 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.79, C:C.100, C:A.106, C:E.107, C:C.133, C:Y.154 Water bridges: C:H.99 Salt bridges: C:R.60, C:H.99, C:R.155 pi-Stacking: C:H.105 DDN.23: 17 residues within 4Å: Chain D: C.58, R.60, A.61, V.63, N.79, H.99, C.100, T.103, H.105, A.106, E.107, P.132, C.133, C.136, Y.154, R.155 Ligands: ZN.20 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.79, D:C.100, D:A.106, D:C.133, D:Y.154 Salt bridges: D:R.60, D:H.99, D:R.155 pi-Stacking: D:H.105 DDN.29: 18 residues within 4Å: Chain E: C.58, R.60, A.61, V.63, N.79, H.99, C.100, T.103, H.105, A.106, E.107, F.131, P.132, C.133, C.136, Y.154, R.155 Ligands: ZN.26 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.79, E:C.100, E:T.103, E:A.106, E:C.133 Water bridges: E:Y.154 Salt bridges: E:R.60, E:H.99, E:R.155 pi-Stacking: E:H.105 DDN.35: 17 residues within 4Å: Chain F: C.58, R.60, A.61, V.63, N.79, H.99, C.100, T.103, H.105, A.106, E.107, P.132, C.133, C.136, Y.154, R.155 Ligands: ZN.32 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:N.79, F:C.100, F:T.103, F:A.106, F:C.133 Salt bridges: F:R.60, F:H.99, F:R.155 pi-Stacking: F:H.105

6 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.6: 4 residues within 4Å: Chain D: S.53, K.54, S.56, Y.62 1 PLIP interactions: 1 interactions with chain D Water bridges: D:K.54 DIO.12: 4 residues within 4Å: Chain B: S.53, K.54, S.56, Y.62 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.54, B:K.54 DIO.18: 5 residues within 4Å: Chain B: R.38 Chain C: S.53, K.54, S.56, Y.62 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.54 DIO.24: 4 residues within 4Å: Chain A: S.53, K.54, S.56, Y.62 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.54 DIO.30: 4 residues within 4Å: Chain E: S.53, K.54, S.56, Y.62 2 PLIP interactions: 2 interactions with chain E Water bridges: E:K.54, E:K.54 DIO.36: 5 residues within 4Å: Chain E: R.38 Chain F: S.53, K.54, S.56, Y.62 1 PLIP interactions: 1 interactions with chain F Water bridges: F:K.54

Links

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Citation

Hou, H.F. et al., Crystal structures of Streptococcus mutans 2'-deoxycytidylate deaminase and its complex with substrate analog and allosteric regulator dCTP x Mg2+. J.Mol.Biol. (2008)

Release Date

2007-09-11

Peptides

deoxycytidylate deaminase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

deoxycytidylate deaminase

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