SMTL ID : 5c2o.1

Crystal structure of Streptococcus mutans Deoxycytidylate Deaminase complexed with dTTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.58, A:C.88, A:C.100 ZN.2: 3 residues within 4Å: Chain A: H.105, C.133, C.136 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.105, A:C.133, A:C.136, H2O.1 ZN.5: 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.6: 3 residues within 4Å: Chain B: H.105, C.133, C.136 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.105, B:C.133, B:C.136, H2O.3 ZN.9: 4 residues within 4Å: Chain C: C.58, C.88, H.93, C.100 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.58, C:C.88, C:C.100 ZN.10: 3 residues within 4Å: Chain C: H.105, C.133, C.136 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.105, C:C.133, C:C.136, H2O.5 ZN.13: 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.14: 3 residues within 4Å: Chain D: H.105, C.133, C.136 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.105, D:C.133, D:C.136, H2O.6 ZN.17: 4 residues within 4Å: Chain E: C.58, C.88, H.93, C.100 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.58, E:C.88, E:C.100 ZN.18: 3 residues within 4Å: Chain E: H.105, C.133, C.136 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.105, E:C.133, E:C.136, H2O.9 ZN.21: 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.22: 3 residues within 4Å: Chain F: H.105, C.133, C.136 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.105, F:C.133, F:C.136, H2O.10

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

MG.3: 1 residues within 4Å: Ligands: TTP.4 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: N.87 Ligands: TTP.8 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: TTP.12 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: N.87 Ligands: TTP.16 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Ligands: TTP.20 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain F: N.87 Ligands: TTP.24 No protein-ligand interaction detected (PLIP)

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

TTP.4: 17 residues within 4Å: Chain A: R.55, T.57, T.76, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109, Q.113 Chain B: Q.142 Chain F: W.41, N.71, R.72 Ligands: MG.3 22 PLIP interactions: 19 interactions with chain A, 2 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: A:Y.78, F:W.41 Hydrogen bonds: A:T.76, A:T.76, A:Y.78, A:Y.78, A:Y.78, A:G.81, A:D.84, A:D.84, A:N.87, A:N.109, B:Q.142 Water bridges: A:R.55, A:R.55, A:T.76, A:G.81, A:T.85, A:Q.113, A:Q.113, F:N.71 Salt bridges: A:R.55 TTP.8: 17 residues within 4Å: Chain A: Q.142 Chain B: R.55, T.57, T.76, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109, Q.113 Chain C: W.41, N.71, R.72 Ligands: MG.7 20 PLIP interactions: 3 interactions with chain C, 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:W.41, B:Y.78 Water bridges: C:W.41, C:N.71, B:R.55, B:R.55, B:R.55, B:T.76, B:Y.78, B:G.81 Hydrogen bonds: B:T.76, B:Y.78, B:Y.78, B:G.81, B:D.84, B:D.84, B:N.87, B:N.109, A:Q.142 Salt bridges: B:R.55 TTP.12: 17 residues within 4Å: Chain B: W.41, N.71, R.72 Chain C: R.55, T.57, T.76, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109, Q.113 Chain D: Q.142 Ligands: MG.11 20 PLIP interactions: 17 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:Y.78, B:W.41 Hydrogen bonds: C:T.76, C:Y.78, C:Y.78, C:G.81, C:D.84, C:D.84, C:N.87, C:N.109, D:Q.142 Water bridges: C:R.55, C:R.55, C:T.76, C:G.81, C:T.85, C:Q.113, C:Q.113, B:N.71 Salt bridges: C:R.55 TTP.16: 17 residues within 4Å: Chain C: Q.142 Chain D: R.55, T.57, T.76, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109, Q.113 Chain E: W.41, N.71, R.72 Ligands: MG.15 21 PLIP interactions: 17 interactions with chain D, 1 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: D:Y.78, E:W.41 Hydrogen bonds: D:T.76, D:Y.78, D:G.81, D:D.84, D:D.84, D:D.84, D:N.87, D:N.109, C:Q.142 Water bridges: D:R.55, D:R.55, D:R.55, D:T.76, D:Y.78, D:G.81, D:N.87, E:W.41, E:N.71 Salt bridges: D:R.55 TTP.20: 17 residues within 4Å: Chain D: W.41, N.71, R.72 Chain E: R.55, T.57, T.76, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109, Q.113 Chain F: Q.142 Ligands: MG.19 23 PLIP interactions: 2 interactions with chain D, 20 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: D:W.41, E:Y.78 Water bridges: D:N.71, E:R.55, E:R.55, E:T.76, E:G.81, E:T.85, E:Q.113, E:Q.113 Hydrogen bonds: E:T.76, E:T.76, E:Y.78, E:Y.78, E:Y.78, E:G.81, E:D.84, E:D.84, E:D.84, E:N.87, E:N.109, F:Q.142 Salt bridges: E:R.55 TTP.24: 17 residues within 4Å: Chain A: W.41, N.71, R.72 Chain E: Q.142 Chain F: R.55, T.57, T.76, G.77, Y.78, G.80, G.81, A.83, D.84, N.87, N.109, Q.113 Ligands: MG.23 19 PLIP interactions: 15 interactions with chain F, 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: F:Y.78, A:W.41 Hydrogen bonds: F:T.76, F:Y.78, F:G.81, F:D.84, F:D.84, F:N.87, F:N.109, E:Q.142 Water bridges: F:R.55, F:R.55, F:R.55, F:T.76, F:Y.78, F:G.81, A:W.41, A:N.71 Salt bridges: F:R.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Mechanism of the allosteric regulation of Streptococcus mutans 2'-deoxycytidylate deaminase. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-07-13

Peptides

Putative deoxycytidylate deaminase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Putative deoxycytidylate deaminase

Related Entries With Identical Sequence