SMTL ID : 7mca.1

Structure of the S. cerevisiae origin recognition complex bound to the replication initiator Cdc6 and the ARS1 origin DNA.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.486, D.566, E.567 Chain D: R.267 Ligands: AGS.2 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain D: T.109, D.217 Chain E: E.154 Ligands: AGS.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain E: T.44, D.133 Ligands: AGS.5 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.44, E:D.133 MG.8: 2 residues within 4Å: Chain I: T.115 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.115

4 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Covalent)(Non-covalent)

AGS.2: 20 residues within 4Å: Chain A: S.432, A.451, P.481, G.482, V.483, G.484, K.485, T.486, L.487, E.567, Y.627, I.635, R.639, A.703, R.704, L.707 Chain D: H.240, R.263, R.267 Ligands: MG.1 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.432, A:G.482, A:G.482, A:V.483, A:G.484, A:K.485, A:T.486, A:L.487, A:E.567, A:N.600, A:Y.627, A:Y.627, A:R.639, A:R.704, D:H.240, D:R.267 Salt bridges: A:K.485, A:K.485, A:R.704, A:R.704 AGS.3: 13 residues within 4Å: Chain D: Y.61, G.62, P.103, R.104, Q.105, S.106, Y.107, K.108, T.109, Y.110, D.113, K.338 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:R.104, D:Q.105, D:Q.105, D:S.106, D:Y.107, D:K.108, D:T.109, D:T.109, D:Y.110, D:D.113 Salt bridges: D:K.108 pi-Stacking: D:Y.110, D:Y.110 AGS.5: 15 residues within 4Å: Chain E: V.8, Y.38, G.40, T.41, G.42, K.43, T.44, Y.45, L.171, Y.192, M.203, S.204, I.255, F.256 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.40, E:T.41, E:G.42, E:K.43, E:K.43, E:T.44, E:T.44, E:Y.45, E:Y.192, E:Y.192 Salt bridges: E:K.43 pi-Stacking: E:Y.45 AGS.7: 21 residues within 4Å: Chain A: Y.580, K.612, R.616 Chain I: N.72, A.80, R.81, P.109, P.110, G.111, T.112, G.113, K.114, T.115, A.116, N.263, S.264, M.296, L.331, R.332, F.335 Ligands: MG.8 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain A Hydrogen bonds: I:A.80, I:T.112, I:G.113, I:K.114, I:T.115, A:K.612 Salt bridges: I:R.332, I:R.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, X. et al., The structure of ORC-Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6. Nat Commun (2021)

Release Date

2021-06-02

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

Related Entries With Identical Sequence