SMTL ID : 7tjk.1

S. cerevisiae ORC bound to 84 bp ARS1 DNA and Cdc6 (state 2) with docked Orc6 N-terminal domain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-mer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 22 residues within 4Å: Chain A: S.435, L.452, P.453, R.455, T.483, P.484, G.485, V.486, G.487, K.488, T.489, L.490, E.570, Y.630, I.638, R.642, A.706, R.707 Chain D: H.243, R.266, R.270 Ligands: MG.2 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:S.435, A:T.483, A:G.485, A:V.486, A:G.487, A:K.488, A:T.489, A:L.490, A:Y.630, A:Y.630, A:R.642, D:H.243 Water bridges: A:K.488, A:R.707, A:R.707, D:Y.235 Salt bridges: A:K.488, A:K.488, A:R.707, A:R.707, A:R.707, D:R.270 ATP.3: 17 residues within 4Å: Chain D: Y.64, G.65, K.72, P.106, R.107, Q.108, S.109, Y.110, K.111, T.112, Y.113, D.116, P.338, K.341 Chain E: K.151, K.158 Ligands: MG.4 22 PLIP interactions: 17 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:K.72, D:Q.108, D:Q.108, D:S.109, D:Y.110, D:K.111, D:T.112, D:Y.113, D:D.116, D:D.116, D:K.341, E:K.158 Water bridges: D:R.107, D:R.107, E:K.151, E:K.151 Salt bridges: D:R.107, D:K.111, D:K.111, E:K.151, E:K.151 pi-Stacking: D:Y.113 ATP.5: 15 residues within 4Å: Chain E: V.8, Y.38, S.39, G.40, T.41, G.42, K.43, T.44, Y.45, L.171, Y.192, I.200, M.203, F.256 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.40, E:T.41, E:G.42, E:K.43, E:T.44, E:T.44, E:Y.45, E:Y.192, E:Y.192 Water bridges: E:T.44 Salt bridges: E:K.43, E:K.43 pi-Stacking: E:Y.45, E:Y.45 ATP.7: 21 residues within 4Å: Chain A: R.619 Chain I: K.67, L.71, L.81, P.82, R.84, P.112, P.113, G.114, T.115, G.116, K.117, T.118, A.119, E.227, N.266, Y.294, I.302, L.334, R.335 Ligands: MG.8 22 PLIP interactions: 1 interactions with chain A, 21 interactions with chain I Salt bridges: A:R.619, I:K.117, I:K.117, I:R.335, I:R.335, I:R.335 Hydrogen bonds: I:K.67, I:G.114, I:T.115, I:T.115, I:G.116, I:K.117, I:T.118, I:A.119, I:E.227, I:N.266, I:Y.294, I:Y.294 Water bridges: I:K.117, I:K.117, I:R.335, I:R.335

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.489, D.569, E.570 Chain D: R.270 Ligands: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.489, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain D: T.112 Chain E: K.151 Ligands: ATP.3 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.112, H2O.3, H2O.4, H2O.4 MG.6: 3 residues within 4Å: Chain E: T.44, D.133 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.44, H2O.4, H2O.4, H2O.4 MG.8: 5 residues within 4Å: Chain A: R.619 Chain I: T.118, D.226, E.227 Ligands: ATP.7 3 PLIP interactions: 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:T.118, H2O.5, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, J.M. et al., A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6. Nat Commun (2022)

Release Date

2022-10-05

Peptides

Origin recognition complex subunit 1: A
Origin recognition complex subunit 2: B
Origin recognition complex subunit 3: C
Origin recognition complex subunit 4: D
Origin recognition complex subunit 5: E
Origin recognition complex subunit 6: F
Cell division control protein 6: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

I
I

Origin recognition complex subunit 1

Origin recognition complex subunit 2

Origin recognition complex subunit 3

Origin recognition complex subunit 4

Origin recognition complex subunit 5

Origin recognition complex subunit 6

Cell division control protein 6

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