SMTL ID : 8gmt.1

Structure of UmuD in complex with RecA filament

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

1 x DT- DT- DT- DT- DT- DT: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')(Non-covalent)

DT-DT-DT-DT-DT-DT.1: 24 residues within 4Å: Chain C: M.165, A.169, R.170, S.173, R.177, R.197, M.198, K.199, I.200, T.210, G.212, G.213, N.214 Chain D: A.169, R.170, R.197, M.198, K.199, I.200, G.201, T.211, G.212, G.213, N.214 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain C: T.74, E.97, D.145, S.146 Ligands: AGS.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.74, C:E.97 MG.4: 4 residues within 4Å: Chain D: T.74, E.97, D.145 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.74

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

AGS.3: 12 residues within 4Å: Chain C: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, Y.265 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.70, C:S.71, C:G.72, C:K.73, C:T.74, C:T.74, C:T.74, C:T.75, C:D.101 Salt bridges: C:K.73 pi-Stacking: C:Y.104, C:Y.104 AGS.5: 20 residues within 4Å: Chain C: F.218, K.249, N.250, K.251, I.252, A.253, A.254, P.255 Chain D: E.69, S.70, S.71, G.72, K.73, T.74, T.75, E.97, D.101, Y.104, Y.265 Ligands: MG.4 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:S.70, D:S.71, D:G.72, D:K.73, D:T.74, D:T.75, C:K.249, C:K.251, C:K.251, C:K.251 Salt bridges: D:K.73 pi-Stacking: D:Y.104, D:Y.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, B. et al., Structural basis for regulation of SOS response in bacteria. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2022-12-21

Peptides

DNA polymerase V subunit UmuD: AB
Protein RecA: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
F

D
G

DNA polymerase V subunit UmuD

Protein RecA

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