SMTL ID : 5zr1.1

Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

AGS.1: 21 residues within 4Å: Chain A: S.432, L.449, P.450, P.481, G.482, V.483, G.484, K.485, T.486, L.487, E.567, N.600, Y.627, I.635, R.639, A.703, R.704 Chain D: H.240, R.263, R.267 Ligands: MG.2 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.432, A:G.482, A:V.483, A:G.484, A:K.485, A:T.486, A:L.487, A:E.567, A:Y.627, A:Y.627, A:R.639, A:R.639, A:R.704, A:R.704, D:R.267, D:R.267 Salt bridges: A:K.485, A:R.704, A:R.704 AGS.3: 14 residues within 4Å: Chain D: Y.61, G.62, K.69, R.104, Q.105, S.106, Y.107, K.108, T.109, Y.110, D.113, K.338 Chain E: K.151 Ligands: MG.4 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:K.69, 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, D:D.113, D:K.338, E:K.151, E:K.151 Salt bridges: D:K.108 pi-Stacking: D:Y.110 AGS.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, I.255, F.256 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:F.10, E:G.40, E:T.41, 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, E:Y.45

3 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, N. et al., Structure of the origin recognition complex bound to DNA replication origin. Nature (2018)

Release Date

2018-07-11

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

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

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