SMTL ID : 7pfo.1

Core human replisome

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.2221, C.2224, C.2236, C.2238 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.2221, A:C.2224, A:C.2236, A:C.2238 ZN.3: 4 residues within 4Å: Chain C: C.306, C.309, C.328, C.331 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.306, C:C.309, C:C.328, C:C.331 ZN.4: 4 residues within 4Å: Chain D: C.158, C.161, C.180, C.185 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.158, D:C.161, D:C.180, D:C.185 ZN.5: 4 residues within 4Å: Chain E: C.184, C.187, C.206, C.211 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.184, E:C.187, E:C.206, E:C.211 ZN.8: 3 residues within 4Å: Chain G: C.329, C.332, C.355 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:C.332, G:C.355 ZN.11: 5 residues within 4Å: Chain H: C.172, S.174, C.175, C.197, C.207 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.172, H:C.175, H:C.197, H:C.207

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain B: N.421, R.425, K.483 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.421 Salt bridges: B:R.425, B:K.483

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

ANP.6: 22 residues within 4Å: Chain F: S.306, I.307, H.308, D.346, P.347, S.348, V.349, A.350, K.351, S.352, Q.353, N.453, V.501 Chain H: R.371, E.463, Q.464, T.509, R.513, V.610, R.611, E.614 Ligands: MG.7 21 PLIP interactions: 13 interactions with chain F, 8 interactions with chain H Hydrogen bonds: F:H.308, F:H.308, F:S.348, F:V.349, F:A.350, F:K.351, F:K.351, F:K.351, F:S.352, F:S.352, F:Q.353, F:Q.353, F:N.453, H:E.463, H:T.509, H:T.509, H:R.513, H:R.513, H:R.611, H:R.611 Salt bridges: H:R.611 ANP.10: 23 residues within 4Å: Chain D: E.478, Q.479, P.525, R.529, V.618, R.619, E.622 Chain G: S.484, I.485, Y.486, H.488, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, E.588, N.631, L.675, V.679 Ligands: MG.9 21 PLIP interactions: 15 interactions with chain G, 6 interactions with chain D Hydrogen bonds: G:Y.486, G:Y.486, G:G.526, G:T.527, G:T.527, G:A.528, G:K.529, G:K.529, G:K.529, G:K.529, G:S.530, G:Q.531, G:Q.531, G:Q.531, G:N.631, D:Q.479, D:R.529, D:R.529, D:R.619, D:R.619 Salt bridges: D:R.619 ANP.12: 24 residues within 4Å: Chain G: H.511, V.513, E.605, Q.606, R.656, T.763, V.764, R.765, E.768 Chain H: S.342, I.343, F.344, D.382, P.383, G.384, T.385, A.386, K.387, S.388, Q.389, E.446, N.489, L.532 Ligands: MG.13 23 PLIP interactions: 9 interactions with chain G, 14 interactions with chain H Hydrogen bonds: G:H.511, G:E.605, G:Q.606, G:R.656, G:R.656, G:T.763, G:R.765, G:R.765, H:F.344, H:F.344, H:G.384, H:T.385, H:T.385, H:A.386, H:K.387, H:K.387, H:K.387, H:S.388, H:S.388, H:Q.389, H:Q.389, H:N.489 Salt bridges: G:R.765

3 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain F: S.352, D.409 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.352 MG.9: 4 residues within 4Å: Chain G: S.530, D.587, E.588 Ligands: ANP.10 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:S.530, G:E.588 MG.13: 5 residues within 4Å: Chain G: R.656 Chain H: S.388, D.445, E.446 Ligands: ANP.12 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:S.388, H:E.446

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, M.L. et al., Structure of a human replisome shows the organisation and interactions of a DNA replication machine. Embo J. (2021)

Release Date

2021-11-10

Peptides

DNA polymerase epsilon catalytic subunit A: A
DNA polymerase epsilon subunit 2: B
DNA replication licensing factor MCM4: C
DNA replication licensing factor MCM6: D
DNA replication licensing factor MCM7: E
DNA replication licensing factor MCM3: F
DNA replication licensing factor MCM2: G
DNA replication licensing factor MCM5: H
DNA replication complex GINS protein PSF1: I
DNA replication complex GINS protein PSF2: J
DNA replication complex GINS protein PSF3: K
DNA replication complex GINS protein SLD5: L
Cell division control protein 45 homolog,Cell division control protein 45 homolog: M
Protein timeless homolog: N
TIMELESS-interacting protein: O
WD repeat and HMG-box DNA-binding protein 1: QRS
Claspin: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
4

D
6

E
7

F
3

G
2

H
5

I
D

J
E

K
F

L
G

M
C

N
K

O
L

Q
H

R
I

S
J

U
Q

DNA polymerase epsilon catalytic subunit A

DNA polymerase epsilon subunit 2

DNA replication licensing factor MCM4

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

DNA replication licensing factor MCM3

DNA replication licensing factor MCM2

DNA replication licensing factor MCM5

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 homolog,Cell division control protein 45 homolog

Protein timeless homolog

TIMELESS-interacting protein

WD repeat and HMG-box DNA-binding protein 1

Claspin

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