SMTL ID : 7u1p.1

RFC:PCNA bound to DNA with a ssDNA gap of five nucleotides

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

AGS.1: 18 residues within 4Å: Chain A: T.299, A.303, P.304, V.310, C.311, P.355, G.356, I.357, G.358, K.359, T.360, T.361, N.456, I.514, R.515 Chain B: E.132, R.157 Ligands: MG.2 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.302, A:C.311, A:G.356, A:I.357, A:I.357, A:G.358, A:K.359, A:T.360, A:T.360, A:T.361, A:T.361, A:R.515, A:R.515, B:S.156, B:R.157, B:R.157 Salt bridges: A:K.359, A:R.515, A:R.515 AGS.5: 23 residues within 4Å: Chain C: V.16, Y.19, R.20, P.21, E.26, V.27, Y.28, P.55, G.56, T.57, G.58, K.59, T.60, S.61, N.148, L.169, M.205, R.206, L.209 Chain D: E.158, P.179, R.183 Ligands: MG.6 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.19, C:R.20, C:Y.28, C:G.56, C:T.57, C:T.57, C:T.57, C:T.57, C:G.58, C:K.59, C:T.60, C:T.60, C:S.61, C:S.61, C:R.206, C:R.206, D:R.183, D:R.183 Salt bridges: C:R.20, C:K.59, C:R.206, C:R.206 AGS.7: 24 residues within 4Å: Chain D: V.28, Y.31, R.32, P.33, E.38, V.39, T.40, P.67, G.68, T.69, G.70, K.71, T.72, S.73, N.171, L.192, L.228, R.229, I.232 Chain E: R.155, E.159, P.180, R.184 Ligands: MG.8 23 PLIP interactions: 19 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:Y.31, D:R.32, D:T.40, D:G.68, D:T.69, D:T.69, D:T.69, D:G.70, D:K.71, D:T.72, D:T.72, D:S.73, D:S.73, D:R.229, D:R.229, E:R.155, E:R.155, E:R.184, E:R.184 Salt bridges: D:R.32, D:K.71, D:R.229, D:R.229

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.360, D.424 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.360 MG.4: 4 residues within 4Å: Chain B: T.56, D.114, E.115 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.56 MG.6: 4 residues within 4Å: Chain C: T.60, E.118 Chain D: R.183 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.60 MG.8: 3 residues within 4Å: Chain D: T.72 Chain E: R.184 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.72

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 21 residues within 4Å: Chain B: V.12, Y.15, R.16, P.17, I.23, V.24, G.25, M.50, P.51, G.52, I.53, G.54, K.55, T.56, T.57, L.166, R.174, M.202, R.203 Chain C: E.135 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Y.15, B:R.16, B:V.24, B:G.25, B:M.50, B:G.52, B:I.53, B:I.53, B:G.54, B:K.55, B:T.56, B:T.57, B:T.57 Salt bridges: B:R.16, B:K.55, B:R.203, B:R.203 ADP.9: 20 residues within 4Å: Chain A: S.695 Chain E: V.5, Y.8, R.9, P.10, 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 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:Y.8, E:R.9, E:S.17, E:S.17, E:H.18, E:N.45, E:G.46, E:T.47, E:G.48, E:K.49, E:K.50, E:T.51, E:R.52, E:R.52 Salt bridges: E:K.49, E:R.231, E:R.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA. Elife (2022)

Release Date

2022-07-06

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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