SMTL ID : 4ykl.1

Hnt3 in complex with DNA and guanosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.168, C.171, H.185, E.189 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.168, A:C.171, A:H.185, A:E.189 ZN.9: 4 residues within 4Å: Chain C: C.168, C.171, H.185, E.189 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.168, C:C.171, C:H.185, C:E.189

2 x GMP: GUANOSINE(Non-covalent)

GMP.2: 13 residues within 4Å: Chain A: L.6, Y.9, R.30, D.31, M.32, F.33, K.35, H.39, M.111, H.115, H.117 Chain B: G.1, A.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.9, A:Y.9, A:Y.9, A:M.32, A:K.35, A:K.35, A:H.106 Salt bridges: A:D.31 GMP.10: 13 residues within 4Å: Chain C: L.6, Y.9, R.30, D.31, M.32, F.33, K.35, H.39, M.111, H.115, H.117 Chain D: G.1, A.2 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.9, C:Y.9, C:M.32, C:K.35, C:K.35 Salt bridges: C:D.31

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: V.72, F.81, C.98 No protein-ligand interaction detected (PLIP) GOL.4: 6 residues within 4Å: Chain A: G.108, S.110, A.132, H.133, F.141 Chain B: G.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.110, A:S.110 Water bridges: A:H.133, A:H.133 GOL.5: 4 residues within 4Å: Chain A: H.185, E.188, E.189, D.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.188, A:D.192 GOL.6: 3 residues within 4Å: Chain A: S.70, Y.71, D.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.70, A:D.75 Water bridges: A:Y.71 GOL.11: 3 residues within 4Å: Chain C: V.72, F.81, C.98 No protein-ligand interaction detected (PLIP) GOL.12: 6 residues within 4Å: Chain C: G.108, S.110, A.132, H.133, F.141 Chain D: G.1 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.110, C:S.110 Water bridges: C:H.133, C:H.133 GOL.13: 4 residues within 4Å: Chain C: H.185, E.188, E.189, D.192 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.188, C:E.188, C:D.192 GOL.14: 3 residues within 4Å: Chain C: S.70, Y.71, D.75 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.70, C:D.75

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain A: E.66, V.69, S.70 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: K.129 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: E.66, V.69, S.70 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain C: K.129 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chauleau, M. et al., DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition. Nucleic Acids Res. (2015)

Release Date

2015-06-03

Peptides

Aprataxin-like protein: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
B

Aprataxin-like protein

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