SMTL ID : 4cei.1

Crystal structure of ADPNP-bound AddAB with a forked DNA substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

ANP.1: 20 residues within 4Å: Chain A: T.10, W.11, Q.15, A.32, G.33, S.34, G.35, K.36, T.37, A.38, R.76, E.408, Q.441, F.478, R.479, K.573, G.798, E.800, R.873 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:T.10, A:Q.15, A:G.33, A:S.34, A:G.35, A:K.36, A:K.36, A:K.36, A:T.37, A:T.37, A:A.38, A:E.408, A:Q.441, A:Q.441, A:R.479, A:R.479, A:K.573, A:E.800, A:R.873, A:R.873 Water bridges: A:R.76, A:R.76, A:E.408 Salt bridges: A:R.76, A:R.479 pi-Stacking: A:F.478 ANP.4: 15 residues within 4Å: Chain B: R.9, S.10, G.11, S.12, G.13, K.14, T.15, K.16, T.236, E.282, R.283, Y.599, G.600, M.656 Ligands: MG.5 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.10, B:G.11, B:S.12, B:G.13, B:K.14, B:K.14, B:K.14, B:T.15, B:T.15, B:T.15, B:K.16, B:T.236, B:R.283, B:R.283 Water bridges: B:S.234, B:T.236, B:T.236 Salt bridges: B:R.283

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.37, D.407, E.408 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.37, H2O.1, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: T.15, D.208 Ligands: ANP.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.15, H2O.1, H2O.1, H2O.1

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.3: 10 residues within 4Å: Chain B: C.801, S.804, I.1110, P.1112, P.1120, C.1121, C.1124, F.1126, K.1127, C.1130 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.801, B:C.1121, B:C.1124, B:C.1130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krajewski, W.W. et al., Structural Basis for Translocation by Addab Helicase-Nuclease and its Arrest at Chi Sites. Nature (2014)

Release Date

2014-03-12

Peptides

ATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT A: A
ATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT A

ATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT B

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