SMTL ID : 7pfo.1

Core human replisome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.329, K.331, C.332, C.352, C.355 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.329, A:C.332, A:C.355 ZN.6: 6 residues within 4Å: Chain C: C.306, V.308, C.309, H.311, 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.7: 5 residues within 4Å: Chain D: C.172, S.174, C.175, C.197, C.207 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.172, D:C.175, D:C.197, D:C.207 ZN.10: 7 residues within 4Å: Chain E: C.158, D.160, C.161, C.180, N.182, C.185, N.187 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.158, E:C.161, E:C.180, E:C.185 ZN.11: 5 residues within 4Å: Chain F: C.184, C.187, C.206, S.208, C.211 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.184, F:C.187, F:C.206, F:C.211

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: K.529, S.530, D.587, E.588 Chain E: R.529, R.619 Ligands: ANP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.530, A:E.588 MG.5: 5 residues within 4Å: Chain B: S.352 Chain D: Q.464, R.513, R.611 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.352 MG.9: 5 residues within 4Å: Chain A: R.656 Chain D: S.388, D.445, E.446 Ligands: ANP.8 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:S.388, D:D.445, D:E.446, D:E.446

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

ANP.3: 26 residues within 4Å: Chain A: S.484, I.485, Y.486, H.488, D.524, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, E.588, N.631, L.675, F.678, V.679 Chain E: L.386, E.478, Q.479, P.525, R.529, V.618, R.619, E.622 Ligands: MG.2 21 PLIP interactions: 13 interactions with chain A, 8 interactions with chain E Hydrogen bonds: A:Y.486, A:Y.486, A:H.488, A:G.526, A:T.527, A:A.528, A:K.529, A:K.529, A:S.530, A:S.530, A:Q.531, A:Q.531, A:N.631, E:Q.479, E:R.529, E:R.529, E:R.619, E:R.619, E:E.622, E:E.622 Salt bridges: E:R.619 ANP.4: 25 residues within 4Å: Chain B: S.306, I.307, H.308, H.310, D.346, P.347, S.348, V.349, A.350, K.351, S.352, Q.353, N.453, I.497, H.500, V.501 Chain D: R.371, E.463, Q.464, T.509, R.513, V.610, R.611, E.614 Ligands: MG.5 22 PLIP interactions: 12 interactions with chain B, 10 interactions with chain D Hydrogen bonds: B:H.308, B:H.308, B:D.346, B:D.346, B:S.348, B:V.349, B:A.350, B:K.351, B:K.351, B:S.352, B:Q.353, B:N.453, D:R.371, D:T.509, D:T.509, D:R.513, D:R.513, D:R.611, D:R.611, D:E.614, D:E.614 Salt bridges: D:R.611 ANP.8: 28 residues within 4Å: Chain A: H.511, V.513, E.605, Q.606, P.652, R.656, T.763, V.764, R.765, E.768 Chain D: 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, H.535, V.536, L.539 Ligands: MG.9 22 PLIP interactions: 8 interactions with chain A, 14 interactions with chain D Hydrogen bonds: A:H.511, A:Q.606, A:R.656, A:R.656, A:R.765, A:R.765, A:E.768, D:F.344, D:F.344, D:D.382, D:G.384, D:T.385, D:A.386, D:K.387, D:K.387, D:S.388, D:S.388, D:S.388, D:Q.389, D:Q.389, D:N.489 Salt bridges: A:R.765

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

SO4.12: 3 residues within 4Å: Chain G: N.421, R.425, K.483 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:N.421 Salt bridges: G:R.425, G:K.483

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

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

O
I

P
J

Q
K

R
L

U
Q

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

DNA replication licensing factor MCM5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

DNA polymerase epsilon subunit 2

DNA polymerase epsilon catalytic subunit A

Cell division control protein 45 homolog

DNA replication complex GINS protein PSF1

DNA replication complex GINS protein PSF2

DNA replication complex GINS protein PSF3

DNA replication complex GINS protein SLD5

WD repeat and HMG-box DNA-binding protein 1

Protein timeless homolog

TIMELESS-interacting protein

Claspin

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