SMTL ID : 6r4u.2 (1 other biounit)

Crystal structure of the Pri1 subunit of human primase bound to fludarabine triphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: R.122, C.124, C.125, I.130, C.131, K.133, C.134 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.124, A:C.125, A:C.131, A:C.134

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 7 residues within 4Å: Chain A: D.112, D.114, S.163, R.166, H.169 Ligands: MN.3, HFD.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.112, A:D.114, H2O.2 MN.3: 6 residues within 4Å: Chain A: D.112, D.114, R.166, D.309 Ligands: MN.2, HFD.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.112, A:D.114, A:D.309, H2O.2

1 x HFD: 2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-a mine(Non-covalent)

HFD.4: 19 residues within 4Å: Chain A: Y.57, R.59, K.80, D.82, D.112, D.114, S.163, R.165, R.166, G.167, H.169, V.312, H.318, L.319, L.320, K.321, H.327 Ligands: MN.2, MN.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Y.57, A:K.80, A:D.82, A:S.163, A:R.165, A:R.166, A:G.167, A:K.321 Water bridges: A:R.166, A:R.166 Salt bridges: A:R.165, A:R.166, A:R.166, A:H.169, A:K.321, A:H.327 Halogen bonds: A:R.59

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: L.207, S.208, E.209, N.284, W.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holzer, S. et al., Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine. Acs Chem.Biol. (2019)

Release Date

2019-09-11

Peptides

DNA primase small subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

DNA primase small subunit

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