SMTL ID : 6r4t.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: R.122, C.124, C.125, 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

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

MN.2: 5 residues within 4Å: Chain A: D.112, D.114, R.166, H.169 Ligands: HEJ.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.112, A:D.112, A:D.114, H2O.1

1 x HEJ: 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine(Non-covalent)

HEJ.3: 17 residues within 4Å: Chain A: Y.57, 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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.80, A:D.82, A:S.163, A:S.163, A:R.165, A:R.166, A:K.321 Water bridges: A:R.166, A:R.166, A:H.169 Salt bridges: A:R.165, A:R.166, A:R.166, A:H.169, A:K.321, A:K.321, A:H.327

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

EDO.4: 3 residues within 4Å: Chain A: T.352, S.354, F.355 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.352, A:S.354 EDO.5: 7 residues within 4Å: Chain A: K.156, H.157, R.158, L.339, H.400, F.401, N.404 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.156, A:R.158, A:F.401, A:N.404

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
A

DNA primase small subunit

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