SMTL ID : 2qby.1

Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

hetero-1-1-mer

Ligands

2 x SPD: SPERMIDINE(Non-functional Binders)

SPD.1: 7 residues within 4Å: Chain A: A.20, G.21, G.22 Chain B: C.11, T.12, A.13, C.14 No protein-ligand interaction detected (PLIP) SPD.2: 2 residues within 4Å: Chain A: T.26, T.27 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-functional Binders)

K.3: 1 residues within 4Å: Chain B: C.10 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain C: T.59, D.135, R.239 Ligands: ADP.5 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.59, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain D: T.59, D.140, N.172 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.59

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 19 residues within 4Å: Chain C: L.14, P.15, L.22, P.23, L.53, T.54, G.55, T.56, G.57, K.58, T.59, A.60, Y.197, I.205, R.209, A.238, R.239, L.242 Ligands: MG.4 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:P.15, C:Y.17, C:L.53, C:G.55, C:T.56, C:G.57, C:K.58, C:T.59, C:T.59, C:A.60, C:Y.197, C:Y.197, C:R.209 Water bridges: C:K.58, C:K.58, C:R.239 Salt bridges: C:K.58, C:R.239, C:R.239 ADP.7: 18 residues within 4Å: Chain D: P.15, F.19, I.22, P.23, L.53, T.54, G.55, T.56, G.57, K.58, T.59, F.60, Y.197, I.205, Y.209, A.238, R.239 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:L.53, D:G.55, D:T.56, D:T.56, D:G.57, D:K.58, D:T.59, D:F.60, D:Y.197, D:Y.209, D:R.239 Water bridges: D:K.58, D:T.59, D:T.59 Salt bridges: D:K.58, D:R.239 pi-Stacking: D:F.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dueber, E.L. et al., Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science (2007)

Release Date

2007-09-11

Peptides

Cell division control protein 6 homolog 1: C
Cell division control protein 6 homolog 3: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

Cell division control protein 6 homolog 1

Cell division control protein 6 homolog 3