SMTL ID : 5x06.1

DNA replication regulation protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.24 Å

Oligo State

hetero-4-4-mer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain C: Q.285 Chain D: R.100, G.101 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.285, C:Q.285 GOL.2: 3 residues within 4Å: Chain D: E.70, K.218 Chain H: T.103 2 PLIP interactions: 2 interactions with chain D Water bridges: D:E.70, D:E.70 GOL.5: 4 residues within 4Å: Chain A: E.70 Chain E: T.103, W.104, F.105 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.103, E:F.105 GOL.10: 3 residues within 4Å: Chain C: E.70, K.218 Chain G: T.103 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:T.103, G:T.103, C:E.70

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

ADP.3: 17 residues within 4Å: Chain E: E.37, S.41, F.42, W.43, G.73, A.74, G.75, R.76, S.77, H.78, L.185, A.193, R.197, M.221, R.222, F.225 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:E.37, E:W.43, E:W.43, E:G.73, E:A.74, E:G.75, E:R.76, E:S.77, E:S.77, E:R.197, E:R.197 Salt bridges: E:R.76 pi-Cation interactions: E:H.78 ADP.6: 17 residues within 4Å: Chain F: E.37, S.41, F.42, W.43, G.73, A.74, G.75, R.76, S.77, H.78, L.185, A.193, R.197, M.221, R.222, F.225 Ligands: MG.7 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:E.37, F:W.43, F:W.43, F:G.73, F:A.74, F:G.75, F:R.76, F:S.77, F:R.197, F:R.197 Salt bridges: F:R.76 pi-Cation interactions: F:H.78 ADP.8: 16 residues within 4Å: Chain G: E.37, S.41, F.42, W.43, E.72, G.73, A.74, G.75, R.76, S.77, H.78, R.197, M.221, R.222, F.225 Ligands: MG.9 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:E.37, G:W.43, G:W.43, G:G.73, G:A.74, G:G.75, G:R.76, G:S.77, G:S.77, G:H.78, G:R.197, G:R.197 Salt bridges: G:R.76 ADP.11: 16 residues within 4Å: Chain H: E.37, S.41, F.42, W.43, G.73, A.74, G.75, R.76, S.77, H.78, L.185, A.193, R.197, R.222, F.225 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:E.37, H:W.43, H:W.43, H:G.73, H:A.74, H:G.75, H:R.76, H:S.77, H:H.78, H:R.197, H:R.197 Water bridges: H:R.76, H:R.76 Salt bridges: H:R.76 pi-Cation interactions: H:H.78

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain E: S.77 Ligands: ADP.3 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:S.77, H2O.1 MG.7: 2 residues within 4Å: Chain F: S.77 Ligands: ADP.6 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:S.77, H2O.1 MG.9: 2 residues within 4Å: Chain G: S.77 Ligands: ADP.8 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:S.77, H2O.2 MG.12: 2 residues within 4Å: Chain H: S.77 Ligands: ADP.11 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:S.77, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J. et al., Replication regulation protein. To Be Published

Release Date

2018-01-24

Peptides

DNA polymerase III subunit beta: ABCD
DnaA regulatory inactivator Hda: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

DNA polymerase III subunit beta

DnaA regulatory inactivator Hda

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