SMTL ID : 7pmk.1

S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation I)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-3-1-1-1-1-1-1-mer

Ligands

3 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 22 residues within 4Å: Chain A: S.504, I.505, Y.506, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, E.608, N.651, L.695, V.699 Chain E: L.565, E.657, Q.658, R.708, V.797, R.798, E.801 Ligands: MG.2 24 PLIP interactions: 9 interactions with chain E, 15 interactions with chain A Hydrogen bonds: E:E.657, E:E.657, E:Q.658, E:P.704, E:R.708, E:R.708, E:R.798, E:R.798, A:Y.506, A:Y.506, A:G.546, A:T.547, A:T.547, A:A.548, A:K.549, A:K.549, A:K.549, A:K.549, A:S.550, A:S.550, A:Q.551, A:Q.551, A:N.651 Salt bridges: E:R.798 ANP.4: 22 residues within 4Å: Chain B: S.408, I.409, Y.410, H.412, P.449, S.450, T.451, A.452, K.453, S.454, Q.455, E.512, N.555, I.599, V.603 Chain D: E.498, Q.499, R.549, I.650, R.651, E.654 Ligands: MG.5 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain D Hydrogen bonds: B:Y.410, B:H.412, B:S.450, B:T.451, B:T.451, B:A.452, B:K.453, B:K.453, B:K.453, B:K.453, B:S.454, B:S.454, B:Q.455, B:Q.455, B:N.555, D:Q.499, D:R.549, D:R.549, D:R.651, D:R.651, D:E.654 Salt bridges: D:R.651 ANP.7: 20 residues within 4Å: Chain A: H.531, E.625, Q.626, R.676, V.807, R.808, E.811 Chain D: S.377, I.378, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, N.524, V.572 Ligands: MG.8 22 PLIP interactions: 14 interactions with chain D, 8 interactions with chain A Hydrogen bonds: D:F.379, D:F.379, D:G.419, D:T.420, D:T.420, D:A.421, D:K.422, D:K.422, D:K.422, D:K.422, D:S.423, D:S.423, D:Q.424, D:N.524, A:H.531, A:E.625, A:Q.626, A:R.676, A:R.676, A:R.808, A:R.808 Salt bridges: A:R.808

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.550, D.607, E.608 Chain E: R.708 Ligands: ANP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.550, A:E.608 MG.5: 4 residues within 4Å: Chain B: S.454, D.511, E.512 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.454 MG.8: 4 residues within 4Å: Chain A: Q.626, R.676 Chain D: S.423 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.423

7 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.341, K.343, C.344, C.364, C.367 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.341, A:C.344, A:C.364, A:C.367 ZN.6: 5 residues within 4Å: Chain C: C.349, V.351, C.352, C.371, C.376 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.349, C:C.352, C:C.371, C:C.376 ZN.9: 4 residues within 4Å: Chain D: C.183, C.186, C.211, C.236 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.183, D:C.186, D:C.211, D:C.236 ZN.10: 5 residues within 4Å: Chain E: C.311, C.314, C.333, C.338, N.340 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:C.314, E:C.333, E:C.338 ZN.11: 4 residues within 4Å: Chain F: C.262, C.265, C.284, C.289 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.262, F:C.265, F:C.284, F:C.289 ZN.12: 4 residues within 4Å: Chain S: C.2108, C.2111, C.2130, C.2133 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.2108, S:C.2111, S:C.2130, S:C.2133 ZN.13: 4 residues within 4Å: Chain S: C.2164, C.2167, C.2179, C.2181 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.2164, S:C.2167, S:C.2179, S:C.2181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jenkyn-Bedford, M. et al., A conserved mechanism for regulating replisome disassembly in eukaryotes. Nature (2021)

Release Date

2021-11-10

Peptides

DNA replication licensing factor MCM2: A
DNA replication licensing factor MCM3: B
DNA replication licensing factor MCM4: C
DNA helicase: D
DNA replication licensing factor MCM6: E
DNA replication licensing factor MCM7: F
DNA replication complex GINS protein PSF1: G
DNA replication complex GINS protein PSF2: H
DNA replication complex GINS protein PSF3: I
DNA replication complex GINS protein SLD5: J
Cell division control protein 45,Cell division control protein 45: K
DNA polymerase alpha-binding protein: LMN
E3 ubiquitin ligase complex SCF subunit: Q
Protein DIA2: R
DNA polymerase epsilon catalytic subunit A: S
DNA polymerase epsilon subunit B: T
Topoisomerase 1-associated factor 1: U
Chromosome segregation in meiosis protein 3: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

G
A

H
B

I
C

J
D

K
E

L
F

M
G

N
H

Q
K

R
L

S
Q

T
R

U
X

V
Y

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

DNA helicase

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

DNA replication complex GINS protein PSF1

DNA replication complex GINS protein PSF2

DNA replication complex GINS protein PSF3

DNA replication complex GINS protein SLD5

Cell division control protein 45,Cell division control protein 45

DNA polymerase alpha-binding protein

E3 ubiquitin ligase complex SCF subunit

Protein DIA2

DNA polymerase epsilon catalytic subunit A

DNA polymerase epsilon subunit B

Topoisomerase 1-associated factor 1

Chromosome segregation in meiosis protein 3

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