SMTL ID : 8dr1.1

Consensus closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

AGS.1: 26 residues within 4Å: Chain A: T.299, Y.302, A.303, P.304, V.310, C.311, P.354, P.355, G.356, I.357, G.358, K.359, T.360, T.361, E.425, N.456, P.478, R.486, I.514, R.515, I.518 Chain B: R.128, E.132, P.153, R.157 Ligands: MG.2 26 PLIP interactions: 23 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.299, A:C.311, A:C.311, A:P.354, A:G.356, A:I.357, A:G.358, A:K.359, A:K.359, A:T.360, A:T.361, A:T.361, A:N.456, A:N.456, A:R.486, A:R.515, B:R.128, B:R.157, B:R.157 Water bridges: A:T.360, A:T.360, A:D.424, A:D.424 Salt bridges: A:K.359, A:R.515, A:R.515 AGS.4: 26 residues within 4Å: Chain B: V.12, Y.15, R.16, P.17, D.22, I.23, V.24, M.50, P.51, G.52, I.53, G.54, K.55, T.56, T.57, N.145, L.166, R.174, M.202, R.203, I.206 Chain C: R.131, E.135, A.156, R.160 Ligands: MG.3 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.15, B:V.24, B:V.24, B:G.52, B:I.53, B:G.54, B:K.55, B:K.55, B:T.56, B:T.57, B:T.57, B:T.57, B:N.145, B:N.145, C:R.131, C:R.160 Water bridges: B:T.56, B:T.56, B:R.203 Salt bridges: B:R.16, B:K.55, B:R.203, B:R.203 AGS.6: 28 residues within 4Å: Chain C: V.16, E.17, Y.19, R.20, P.21, E.26, V.27, Y.28, Q.30, P.54, P.55, G.56, T.57, G.58, K.59, T.60, S.61, N.148, L.169, R.177, M.205, R.206, L.209 Chain D: R.154, E.158, P.179, R.183 Ligands: MG.5 25 PLIP interactions: 5 interactions with chain D, 20 interactions with chain C Hydrogen bonds: D:R.154, D:R.154, D:R.183, D:R.183, C:Y.19, C:Y.28, C:Y.28, C:G.56, C:T.57, C:T.57, C:G.58, C:K.59, C:K.59, C:T.60, C:S.61, C:S.61, C:N.148, C:N.148, C:R.206 Water bridges: D:E.158, C:T.60 Salt bridges: C:R.20, C:K.59, C:R.206, C:R.206 AGS.8: 27 residues within 4Å: Chain D: V.28, Y.31, R.32, P.33, E.38, V.39, T.40, A.41, Q.42, P.67, G.68, T.69, G.70, K.71, T.72, S.73, N.171, L.192, R.200, L.228, R.229, I.232 Chain E: R.155, E.159, P.180, R.184 Ligands: MG.7 25 PLIP interactions: 21 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:Y.31, D:T.40, D:T.40, D:G.68, D:T.69, D:T.69, D:G.70, D:K.71, D:K.71, D:T.72, D:S.73, D:S.73, D:S.73, D:N.171, D:N.171, D:R.229, E:R.155, E:R.184, E:R.184 Water bridges: D:T.72, E:E.159 Salt bridges: D:R.32, D:K.71, D:R.229, D:R.229

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: T.360, D.424, R.515 Chain B: R.128, R.157 Ligands: AGS.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.360, H2O.1, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain B: T.56, R.203 Chain C: R.131, R.160 Ligands: AGS.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.56, H2O.1, H2O.1, H2O.1 MG.5: 5 residues within 4Å: Chain C: T.60, R.206 Chain D: R.154, R.183 Ligands: AGS.6 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.60, H2O.1, H2O.1, H2O.1 MG.7: 4 residues within 4Å: Chain D: T.72, R.229 Chain E: R.184 Ligands: AGS.8 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.72, H2O.1, H2O.1, H2O.1

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.9: 21 residues within 4Å: Chain A: S.695 Chain E: V.5, Y.8, R.9, P.10, A.15, L.16, S.17, H.18, N.45, G.46, T.47, G.48, K.49, K.50, T.51, R.52, I.201, L.230, R.231, L.234 21 PLIP interactions: 20 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.9, E:S.17, E:S.17, E:S.17, E:S.17, E:H.18, E:H.18, E:G.46, E:T.47, E:T.47, E:G.48, E:K.49, E:K.50, E:T.51, E:T.51, E:R.52, E:R.52, A:S.695 Salt bridges: E:K.49, E:R.231, E:R.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schrecker, M. et al., Multistep loading of a DNA sliding clamp onto DNA by replication factor C. Elife (2022)

Release Date

2022-08-17

Peptides

Replication factor C subunit 1: A
Replication factor C subunit 4: B
Replication factor C subunit 3: C
Replication factor C subunit 2: D
Replication factor C subunit 5: E
Proliferating cell nuclear antigen: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Replication factor C subunit 1

Replication factor C subunit 4

Replication factor C subunit 3

Replication factor C subunit 2

Replication factor C subunit 5

Proliferating cell nuclear antigen

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