SMTL ID : 5of3.1

Crystal structure of the heterotrimeric PriSLX primase from S. solfataricus.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)(Covalent)

APC.1: 14 residues within 4Å: Chain A: Y.48, F.74, D.101, D.103, S.173, N.175, R.176, H.179, V.238, R.244, L.245, R.247, H.253 Ligands: MN.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.48, A:S.173, A:N.175, A:N.175, A:R.176, A:R.176, A:H.179, A:H.179, A:R.244, A:R.247, A:R.247 Salt bridges: A:R.176, A:H.253 APC.4: 17 residues within 4Å: Chain A: D.62, R.67 Chain C: Y.48, F.74, D.101, D.103, S.173, N.175, R.176, G.177, H.179, V.238, R.244, L.245, R.247, H.253 Ligands: MN.5 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:Y.48, C:S.173, C:N.175, C:N.175, C:R.176, C:R.244, C:R.247, C:R.247, A:R.67, A:R.67 Salt bridges: C:R.176, C:H.253 pi-Cation interactions: A:R.67, A:R.67 APC.7: 12 residues within 4Å: Chain A: E.89, E.90 Chain E: Q.69, D.70, S.71, R.72, K.73, R.74, L.77, Y.103, W.115 Ligands: MN.8 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.72, E:K.73, E:R.74, E:R.74, E:Y.103, A:E.90 Salt bridges: E:R.72, E:K.73 APC.9: 13 residues within 4Å: Chain C: E.89, E.90 Chain F: Q.69, D.70, S.71, R.72, K.73, R.74, L.77, Y.78, Y.103, W.115 Ligands: MN.10 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:R.72, F:K.73, F:R.74, F:R.74, F:Y.103, F:Y.103, C:E.90 Salt bridges: F:R.72, F:K.73

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

MN.2: 4 residues within 4Å: Chain A: D.101, D.103, H.179 Ligands: APC.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.101, A:D.103 MN.5: 4 residues within 4Å: Chain C: D.101, D.103, H.179 Ligands: APC.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.101, C:D.103 MN.8: 2 residues within 4Å: Chain E: D.70 Ligands: APC.7 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.70, E:D.70 MN.10: 2 residues within 4Å: Chain F: D.70 Ligands: APC.9 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.70, F:D.70

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.116, C.119, C.128, D.131 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.116, A:C.119, A:C.128, A:D.131 ZN.6: 4 residues within 4Å: Chain C: C.116, C.119, C.128, D.131 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.116, C:C.119, C:C.128, C:D.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holzer, S. et al., Primer synthesis by a eukaryotic-like archaeal primase is independent of its Fe-S cluster. Nat Commun (2017)

Release Date

2017-11-29

Peptides

DNA primase small subunit PriS: AC
DNA primase large subunit PriL: BD
Uncharacterized protein: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

E
C

F
F

DNA primase small subunit PriS

DNA primase large subunit PriL

Uncharacterized protein

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