SMTL ID : 2hvv.1

Crystal structure of dCMP deaminase from Streptococcus mutans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

24 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: Y.78, G.80, G.81, N.109 Chain B: Q.142 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain A: K.116 Chain B: N.122 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: C.133, I.134, H.157 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: S.40, W.41 Chain F: R.55 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: T.103, H.105 Chain B: N.135, K.138 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: N.135 Chain B: I.101, T.103, H.105 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: Q.142 Chain B: Y.78, G.80, G.81, N.109 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: S.40, W.41 Chain C: R.55 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain C: Y.78, G.80, G.81, N.109 Chain D: Q.142 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain C: K.116 Chain D: N.122 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain C: C.133, I.134, H.157 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain B: R.55 Chain C: S.40, W.41 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain C: T.103, H.105 Chain D: N.135, K.138 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: N.135 Chain D: I.101, T.103, H.105 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain C: Q.142 Chain D: Y.78, G.80, G.81, N.109 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain D: S.40, W.41 Chain E: R.55 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain E: Y.78, G.80, G.81, N.109 Chain F: Q.142 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain E: K.116 Chain F: N.122 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain E: C.133, I.134, H.157 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain D: R.55 Chain E: S.40, W.41 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain E: T.103, H.105 Chain F: N.135, K.138 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain E: N.135 Chain F: I.101, T.103, H.105 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain E: Q.142 Chain F: Y.78, G.80, G.81, N.109 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain A: R.55 Chain F: S.40, W.41 Ligand excluded by PLIP

12 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.105, E.107, 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.6: 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.11: 5 residues within 4Å: Chain B: C.58, R.60, 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.12: 4 residues within 4Å: Chain B: H.105, E.107, 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.1 ZN.17: 4 residues within 4Å: Chain C: H.105, E.107, 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.2 ZN.18: 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.23: 5 residues within 4Å: Chain D: C.58, R.60, 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.24: 4 residues within 4Å: Chain D: H.105, E.107, 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.2 ZN.29: 4 residues within 4Å: Chain E: H.105, E.107, 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.3 ZN.30: 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.35: 5 residues within 4Å: Chain F: C.58, R.60, 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.36: 4 residues within 4Å: Chain F: H.105, E.107, 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.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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
A

D
B

E
A

F
B

deoxycytidylate deaminase

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