SMTL ID : 3sz5.1

Crystal Structure of LHK-Exo in complex with 5-phosphorylated oligothymidine (dT)4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

3 x DT- DT- DT- DT: 5'-D(P*TP*TP*TP*T)-3'(Non-covalent)

DT-DT-DT-DT.1: 27 residues within 4Å: Chain A: W.8, F.9, R.12, T.17, A.18, S.19, N.58, A.60, M.61, G.64, T.65, E.68, L.88, A.99, S.100, D.102, E.112, I.113, K.114, C.115, P.116, N.117, T.120, Y.134, Q.137 Ligands: MG.2, MG.3 Protein-ligand interaction information (PLIP) not available DT-DT-DT-DT.4: 27 residues within 4Å: Chain B: W.8, F.9, R.12, T.17, A.18, S.19, N.58, A.60, M.61, G.64, T.65, E.68, L.88, A.99, S.100, D.102, E.112, I.113, K.114, C.115, P.116, N.117, T.120, Y.134, Q.137 Ligands: MG.5, MG.6 Protein-ligand interaction information (PLIP) not available DT-DT-DT-DT.7: 27 residues within 4Å: Chain C: W.8, F.9, R.12, T.17, A.18, S.19, N.58, A.60, M.61, G.64, T.65, E.68, L.88, A.99, S.100, D.102, E.112, I.113, K.114, C.115, P.116, N.117, T.120, Y.134, Q.137 Ligands: MG.8, MG.9 Protein-ligand interaction information (PLIP) not available

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.102, E.112, I.113, K.114 Ligands: DT-DT-DT-DT.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.102, A:E.112, A:I.113 MG.3: 6 residues within 4Å: Chain A: S.100, D.102, E.112 Ligands: DT-DT-DT-DT.1, DT-DT-DT-DT.1, MG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.100, A:D.102 MG.5: 6 residues within 4Å: Chain B: D.102, E.112, I.113, K.114 Ligands: DT-DT-DT-DT.4, MG.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.102, B:E.112, B:I.113 MG.6: 6 residues within 4Å: Chain B: S.100, D.102, E.112 Ligands: DT-DT-DT-DT.4, DT-DT-DT-DT.4, MG.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.100, B:D.102 MG.8: 6 residues within 4Å: Chain C: D.102, E.112, I.113, K.114 Ligands: DT-DT-DT-DT.7, MG.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.102, C:E.112, C:I.113 MG.9: 6 residues within 4Å: Chain C: S.100, D.102, E.112 Ligands: DT-DT-DT-DT.7, DT-DT-DT-DT.7, MG.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.100, C:D.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, W. et al., Structural and functional insight into the mechanism of an alkaline exonuclease from Laribacter hongkongensis. Nucleic Acids Res. (2011)

Release Date

2012-02-15

Peptides

Exonuclease: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Exonuclease

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