SMTL ID : 7qvb.1

Crystal structure of the DNA-binding protein DdrC from Deinococcus radiodurans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: T.137, R.140, H.141, Q.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.200 Salt bridges: A:R.140, A:H.141 SO4.2: 4 residues within 4Å: Chain A: T.181, A.183, E.184 Chain B: R.197 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:R.197, B:R.197 Salt bridges: B:R.197 Hydrogen bonds: A:T.181, A:T.181 SO4.3: 1 residues within 4Å: Chain A: R.146 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.146 Salt bridges: A:R.146 SO4.4: 2 residues within 4Å: Chain A: R.85, K.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.85 Water bridges: A:R.84 Salt bridges: A:K.88 SO4.5: 2 residues within 4Å: Chain A: R.219, Q.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.223 Water bridges: A:R.219, A:R.219 SO4.6: 5 residues within 4Å: Chain B: G.15, S.16, V.17, R.85, R.89 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.16, B:S.16 Salt bridges: B:R.85, B:R.89 SO4.7: 5 residues within 4Å: Chain B: P.20, H.28, F.58, A.60, E.63 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.60 Salt bridges: B:H.28 SO4.8: 3 residues within 4Å: Chain A: R.103 Chain B: W.120, R.124 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.120, B:R.124, A:R.103 SO4.9: 3 residues within 4Å: Chain A: R.197 Chain B: R.187, W.225 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.197 Hydrogen bonds: B:W.225 Water bridges: B:R.187 SO4.10: 3 residues within 4Å: Chain B: P.69, D.70, A.73 No protein-ligand interaction detected (PLIP) SO4.11: 8 residues within 4Å: Chain B: S.127, T.128, G.129, A.130, R.131, R.132, A.189, D.192 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.127, B:T.128, B:G.129, B:A.130, B:R.131, B:D.192 Salt bridges: B:R.177 SO4.12: 6 residues within 4Å: Chain B: F.14, L.93, R.96, V.104, Q.107, R.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.107 Salt bridges: B:R.96, B:R.111 SO4.13: 4 residues within 4Å: Chain B: T.137, R.140, H.141, Q.200 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.140, B:H.141 SO4.14: 3 residues within 4Å: Chain B: A.175, T.176, R.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.176, B:R.177, B:R.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banneville, A.S. et al., Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction. Nucleic Acids Res. (2022)

Release Date

2022-06-22

Peptides

DNA damage response protein C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA damage response protein C