SMTL ID : 4f1h.1

Crystal structure of TDP2 from Danio rerio complexed with a single strand DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

hetero-1-1-mer

Ligands

1 x DT- DG- DC- DA- DG: DNA (5'-D(P*TP*GP*CP*AP*G)-3')(Non-covalent)

DT-DG-DC-DA-DG.1: 26 residues within 4Å: Chain A: N.10, L.14, R.96, H.116, S.119, C.120, K.121, D.152, N.154, R.156, R.184, Y.185, W.187, K.195, Y.199, V.200, S.201, R.202, C.203, F.205, H.241 Chain B: N.123, Q.124, Q.126 Ligands: PO4.2, MG.4 Protein-ligand interaction information (PLIP) not available

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 1 residues within 4Å: Ligands: DT-DG-DC-DA-DG.1 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Q.180, H.182, C.183, H.223, M.224, A.225 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.180, A:H.182, A:M.224 Water bridges: A:Q.180 GOL.5: 2 residues within 4Å: Chain A: F.81, L.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.81 GOL.6: 5 residues within 4Å: Chain B: D.158, W.175, R.185, R.205, R.208 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.185, B:R.185, B:R.205, B:R.205, B:R.208, B:R.208 Water bridges: B:A.159 GOL.7: 4 residues within 4Å: Chain B: L.20, A.21, A.47, Y.48 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: E.42 Ligands: DT-DG-DC-DA-DG.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.42, H2O.3, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, K. et al., Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-10-31

Peptides

Tyrosyl-DNA phosphodiesterase 2: A
Tyrosyl-DNA phosphodiesterase 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tyrosyl-DNA phosphodiesterase 2

Tyrosyl-DNA phosphodiesterase 2