SMTL ID : 3gpl.1 (1 other biounit)

Crystal structure of the ternary complex of RecD2 with DNA and ADPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

DT-DT-DT-DT-DT-DT-DT.1: 22 residues within 4Å: Chain A: Q.88, P.240, T.241, G.242, T.258, H.260, R.261, Y.265, G.266, V.321, P.403, M.404, R.405, K.446, N.447, Y.449, N.455, T.495, H.497, R.498, P.517, M.518 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.218 Ligands: ANP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.218, H2O.3, H2O.4, H2O.4

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 16 residues within 4Å: Chain A: G.189, Q.194, G.212, P.213, G.214, T.215, G.216, K.217, S.218, T.219, Q.317, Y.343, R.344, E.503, R.530 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:Q.194, A:Q.194, A:G.214, A:T.215, A:G.216, A:K.217, A:K.217, A:K.217, A:S.218, A:S.218, A:T.219, A:T.219, A:Q.317, A:Q.317, A:Q.317, A:R.344, A:R.344, A:E.503, A:R.530, A:R.530 Water bridges: A:S.218, A:G.501, A:G.501 Salt bridges: A:R.344 pi-Stacking: A:Y.343, A:Y.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saikrishnan, K. et al., Mechanistic basis of 5'-3' translocation in SF1B helicases. Cell(Cambridge,Mass.) (2009)

Release Date

2009-06-16

Peptides

Exodeoxyribonuclease V, subunit RecD, putative: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Exodeoxyribonuclease V, subunit RecD, putative

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