SMTL ID : 4lcn.1

Crytsal structure of NE0047 in complex with 2'-DEOXY-GUANOSINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.79, E.81, C.114, M.116, C.117 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.79, A:C.114, A:C.117, H2O.3 ZN.4: 6 residues within 4Å: Chain B: H.79, E.81, C.114, M.116, C.117 Ligands: EDO.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.79, B:C.114, B:C.117, H2O.3

1 x GNG: 2'-DEOXY-GUANOSINE(Non-covalent)

GNG.2: 13 residues within 4Å: Chain A: F.50, N.68, H.79, A.80, E.81, A.111, E.112, C.114, F.143, D.144, E.145 Chain B: W.123 Ligands: EDO.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.143 Hydrogen bonds: A:N.68, A:A.80, A:E.112, A:D.144 Water bridges: A:H.79, A:T.109, A:A.111, A:C.114, A:C.114 Salt bridges: A:E.81, A:E.145 pi-Stacking: A:F.50, A:F.50, A:H.79

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: N.68, V.70, V.71 Ligands: GNG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.68 Water bridges: A:V.70, A:H.79 EDO.5: 4 residues within 4Å: Chain B: G.10, R.69, P.72, G.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.69 Water bridges: B:P.72 EDO.6: 8 residues within 4Å: Chain B: F.50, H.79, E.81, A.111, E.112, V.138, E.145 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.112 Water bridges: B:N.68, B:H.79, B:C.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bitra, A. et al., Structural basis of the substrate specificity of cytidine deaminase superfamily Guanine deaminase. Biochemistry (2013)

Release Date

2014-01-22

Peptides

Cytidine and deoxycytidylate deaminase zinc-binding region: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytidine and deoxycytidylate deaminase zinc-binding region

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