SMTL ID : 6hpq.1

Crystal structure of human Pif1 helicase in complex with AMP-PNP, brominated crystal form.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 20 residues within 4Å: Chain A: M.3, Q.4, L.5, S.6, Q.9, S.27, A.28, G.29, T.30, G.31, K.32, S.33, Y.34, E.105, Q.144, W.178, R.179, G.357, R.382 Ligands: MG.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:S.6, A:Q.9, A:Q.9, A:S.27, A:G.29, A:T.30, A:T.30, A:G.31, A:K.32, A:K.32, A:S.33, A:Y.34, A:Q.144, A:Q.144, A:R.179, A:R.179, A:R.382, A:R.382 Water bridges: A:S.33, A:S.33, A:S.33, A:G.357, A:G.357, A:T.359, A:T.359 Salt bridges: A:R.179 pi-Stacking: A:W.178, A:W.178, A:W.178 ANP.8: 19 residues within 4Å: Chain B: M.3, Q.4, S.6, Q.9, S.27, A.28, G.29, T.30, G.31, K.32, S.33, Y.34, E.105, Q.144, W.178, R.179, G.357, R.382 Ligands: MG.9 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:S.6, B:Q.9, B:Q.9, B:G.29, B:T.30, B:G.31, B:K.32, B:K.32, B:S.33, B:Y.34, B:Q.144, B:R.179, B:R.179, B:G.357, B:R.382, B:R.382 Water bridges: B:K.32, B:S.33, B:S.33, B:S.33, B:S.33, B:E.105, B:G.357, B:R.384 Salt bridges: B:R.179 pi-Stacking: B:W.178, B:W.178, B:W.178

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.33, E.105 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.33, H2O.6, H2O.8, H2O.9 MG.9: 3 residues within 4Å: Chain B: S.33, E.105 Ligands: ANP.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.33, H2O.28, H2O.31, H2O.32

9 x BR: BROMIDE ION(Non-covalent)(Non-functional Binders)

BR.3: 3 residues within 4Å: Chain A: G.195, C.197, P.396 Ligand excluded by PLIP BR.4: 4 residues within 4Å: Chain A: S.366, L.367, G.368, R.369 Ligand excluded by PLIP BR.5: 5 residues within 4Å: Chain A: Q.227, V.230, M.350, S.351, K.354 Ligand excluded by PLIP BR.6: 4 residues within 4Å: Chain A: K.212, V.213, G.214, R.390 Ligand excluded by PLIP BR.7: 2 residues within 4Å: Chain A: R.14, K.18 Ligand excluded by PLIP BR.10: 3 residues within 4Å: Chain B: G.195, C.197, P.396 Ligand excluded by PLIP BR.11: 4 residues within 4Å: Chain B: S.366, L.367, G.368, R.369 Ligand excluded by PLIP BR.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.13: 3 residues within 4Å: Chain B: P.78, A.80, Q.81 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dehghani-Tafti, S. et al., Structural and functional analysis of the nucleotide and DNA binding activities of the human PIF1 helicase. Nucleic Acids Res. (2019)

Release Date

2019-01-23

Peptides

ATP-dependent DNA helicase PIF1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent DNA helicase PIF1

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