SMTL ID : 6r5d.1 (1 other biounit)

Crystal structure of the Pri1 subunit of human primase bound to dATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: 6 residues within 4Å: Chain A: D.112, D.114, R.166, H.169 Ligands: MN.3, DTP.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, DTP.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.112, A:D.114, A:D.309, H2O.4, H2O.7

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.4: 18 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, MN.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.163, A:R.165, A:R.166, A:G.167, A:K.321 Water bridges: A:K.80, A:R.166, A:R.166, A:H.169, 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 pi-Cation interactions: A:K.80

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

EDO.5: 3 residues within 4Å: Chain A: T.352, S.354, F.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.352, A:T.352, A:S.354 EDO.6: 5 residues within 4Å: Chain A: A.128, D.129, I.130, F.348 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.128, A:I.130 EDO.7: 7 residues within 4Å: Chain A: K.156, H.157, R.158, L.339, H.400, F.401, N.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.158, A:N.404 EDO.8: 3 residues within 4Å: Chain A: E.190, Y.191, K.196 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.191 EDO.9: 5 residues within 4Å: Chain A: R.216, I.219, N.220, K.223, W.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.220, A:K.223 EDO.10: 10 residues within 4Å: Chain A: I.130, Y.162, G.164, R.165, T.330, R.332, P.347, F.348, V.350 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.162, A:Y.162 Water bridges: A:I.130 EDO.11: 5 residues within 4Å: Chain A: K.17, L.18, R.21, R.22, R.384 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.22, A:R.22, A:R.384, A:R.384 Water bridges: A:L.18

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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