SMTL ID : 1sxj.1

Crystal Structure of the Eukaryotic Clamp Loader (Replication Factor C, RFC) Bound to the DNA Sliding Clamp (Proliferating Cell Nuclear Antigen, PCNA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

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

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.91, D.155 Chain B: R.128 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.91 MG.3: 5 residues within 4Å: Chain B: T.56, D.114, E.115 Chain C: R.131 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.56 MG.5: 3 residues within 4Å: Chain C: T.60, D.117 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.60 MG.7: 5 residues within 4Å: Chain D: T.72, D.140, E.141 Chain E: R.155 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.72

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

AGS.2: 21 residues within 4Å: Chain A: T.30, Y.33, A.34, P.35, Q.40, V.41, C.42, P.86, G.87, I.88, G.89, K.90, T.91, T.92, N.187, I.245, R.246 Chain B: R.128, E.132, P.153 Ligands: MG.1 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.30, A:C.42, A:G.87, A:I.88, A:I.88, A:G.89, A:K.90, A:T.91, A:T.92, A:T.92, A:R.246, B:R.128, B:R.128 Salt bridges: A:K.90, A:R.246, A:R.246 AGS.4: 23 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, E.115, N.145, R.174, M.202, R.203 Chain C: R.131, A.156 Ligands: MG.3 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.15, B:R.16, B:V.24, 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, B:E.115, B:R.203, B:R.203, C:R.131, C:R.131 Salt bridges: B:R.16, B:K.55, B:R.203, B:R.203 AGS.6: 23 residues within 4Å: Chain C: V.16, E.17, 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: R.154, E.158 Ligands: MG.5 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.17, C:Y.19, C:Y.28, C:G.56, C:T.57, C:T.57, C:G.58, C:K.59, C:T.60, C:S.61, C:R.206, D:R.154 Salt bridges: C:R.20, C:K.59, C:R.206, C:R.206 AGS.8: 22 residues within 4Å: Chain D: V.28, E.29, Y.31, R.32, P.33, V.39, T.40, A.41, P.67, G.68, T.69, G.70, K.71, T.72, S.73, E.141, N.171, L.228, R.229 Chain E: R.155, P.180 Ligands: MG.7 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:E.29, D:Y.31, D:T.40, D:Q.42, D:G.68, D:T.69, D:T.69, D:G.70, D:K.71, D:T.72, D:T.72, D:S.73, D:E.141, D:R.229, D:R.229, E:R.155, E:R.155 Salt bridges: D:R.32, D:K.71, D:R.229, D:R.229

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

ADP.9: 17 residues within 4Å: Chain E: V.5, R.9, P.10, S.17, H.18, P.44, N.45, G.46, T.47, G.48, K.49, K.50, T.51, I.201, L.230, R.231, L.234 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:V.5, E:S.17, E:S.17, E:H.18, E:G.46, E:T.47, E:G.48, E:K.49, E:K.50, E:T.51 Salt bridges: E:K.49, E:K.50, E:R.231, E:R.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bowman, G.D. et al., Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Nature (2004)

Release Date

2004-06-22

Peptides

Activator 1 95 kDa subunit: A
Activator 1 37 kDa subunit: B
Activator 1 40 kDa subunit: C
Activator 1 41 kDa subunit: D
Activator 1 40 kDa subunit: 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

Activator 1 95 kDa subunit

Activator 1 37 kDa subunit

Activator 1 40 kDa subunit

Activator 1 41 kDa subunit

Activator 1 40 kDa subunit

Proliferating cell nuclear antigen