SMTL ID : 8dqw.1

Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.56, D.114 Chain B: R.131, R.160 Ligands: AGS.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.56, H2O.1, H2O.1, H2O.2 MG.3: 5 residues within 4Å: Chain B: T.60, D.117, R.206 Chain C: R.183 Ligands: AGS.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.60, H2O.3, H2O.4, H2O.5 MG.5: 4 residues within 4Å: Chain C: T.72 Chain D: R.155, R.184 Ligands: AGS.6 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.72, H2O.6, H2O.7, H2O.8 MG.9: 6 residues within 4Å: Chain H: S.116, T.117, K.120, E.187, R.312 Ligands: AGS.8 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:S.116, H2O.14, H2O.14, H2O.15

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

AGS.2: 27 residues within 4Å: Chain A: V.12, E.13, 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 B: R.131, E.135, A.156, R.160 Ligands: MG.1 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.15, A:V.24, A:V.24, A:G.52, A:I.53, A:G.54, A:K.55, A:K.55, A:T.56, A:T.57, A:T.57, A:N.145, A:R.203, B:R.131, B:R.160 Water bridges: A:T.56, A:R.174 Salt bridges: A:R.16, A:K.55, A:R.203, A:R.203 AGS.4: 28 residues within 4Å: Chain B: 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 C: R.154, E.158, P.179, R.183 Ligands: MG.3 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.19, B:Y.28, B:Y.28, B:G.56, B:T.57, B:T.57, B:G.58, B:K.59, B:K.59, B:T.60, B:S.61, B:S.61, B:N.148, B:R.206, C:R.154, C:R.183 Water bridges: B:T.60, B:R.177, B:R.177 Salt bridges: B:R.20, B:K.59, B:R.206, B:R.206 AGS.6: 27 residues within 4Å: Chain C: 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 D: R.155, E.159, P.180, R.184 Ligands: MG.5 24 PLIP interactions: 21 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Y.31, C:T.40, C:T.40, C:G.68, C:T.69, C:T.69, C:G.70, C:K.71, C:K.71, C:T.72, C:T.72, C:S.73, C:S.73, C:N.171, C:N.171, C:R.229, D:R.155, D:R.184, D:R.184 Water bridges: C:R.200 Salt bridges: C:R.32, C:K.71, C:R.229, C:R.229 AGS.8: 25 residues within 4Å: Chain A: R.128, P.153, R.157 Chain H: Y.67, F.70, K.71, P.72, Q.77, V.78, A.79, P.110, S.111, G.112, C.113, S.114, K.115, S.116, T.117, E.187, T.224, H.276, I.311, R.312, I.315 Ligands: MG.9 18 PLIP interactions: 16 interactions with chain H, 2 interactions with chain A Hydrogen bonds: H:Q.77, H:A.79, H:G.112, H:C.113, H:S.114, H:K.115, H:S.116, H:S.116, H:T.117, H:T.117, H:E.187, H:R.312, A:R.128 Water bridges: H:K.115, H:T.224, A:R.128 Salt bridges: H:K.115, H:R.312

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

GDP.7: 21 residues within 4Å: Chain D: V.5, Y.8, R.9, P.10, A.15, L.16, S.17, H.18, P.44, N.45, G.46, T.47, G.48, K.49, K.50, T.51, R.52, I.201, L.230, R.231, L.234 22 PLIP interactions: 21 interactions with chain D, 1 interactions with chain H Hydrogen bonds: D:S.17, D:S.17, D:S.17, D:S.17, D:H.18, D:N.45, D:G.46, D:T.47, D:T.47, D:G.48, D:K.49, D:K.50, D:T.51, D:T.51, D:R.52, D:R.52 Water bridges: D:K.49, D:R.231, H:N.479 Salt bridges: D:K.49, D:R.231, D: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 4: A
Replication factor C subunit 3: B
Replication factor C subunit 2: C
Replication factor C subunit 5: D
DNA damage checkpoint control protein RAD17: E
DDC1 isoform 1: F
DNA damage checkpoint control protein MEC3: G
RAD24 isoform 1: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

F
G

G
H

H
A

Replication factor C subunit 4

Replication factor C subunit 3

Replication factor C subunit 2

Replication factor C subunit 5

DNA damage checkpoint control protein RAD17

DDC1 isoform 1

DNA damage checkpoint control protein MEC3

RAD24 isoform 1

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