SMTL ID : 3ak9.1

Crystal structure of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis, FE-soaked form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-12-mer

Ligands

12 x FE2: FE (II) ION(Non-covalent)

FE2.1: 5 residues within 4Å: Chain A: D.78, E.82 Chain C: K.48, H.51, H.63 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.51, A:D.78, A:E.82, H2O.9, H2O.10 FE2.2: 5 residues within 4Å: Chain B: D.78, E.82 Chain D: K.48, H.51, H.63 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.78, B:E.82, D:H.51, H2O.14, H2O.14 FE2.3: 5 residues within 4Å: Chain A: K.48, H.51, H.63 Chain C: D.78, E.82 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.78, C:E.82, A:H.51, H2O.1, H2O.1 FE2.5: 5 residues within 4Å: Chain B: K.48, H.51, H.63 Chain D: D.78, E.82 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.78, D:E.82, B:H.51, H2O.4, H2O.5 FE2.8: 5 residues within 4Å: Chain E: D.78, E.82 Chain G: K.48, H.51, H.63 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: E:D.78, E:E.82, G:H.51, H2O.18, H2O.27 FE2.10: 5 residues within 4Å: Chain F: D.78, E.82 Chain H: K.48, H.51, H.63 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: F:D.78, F:E.82, H:H.51, H2O.23, H2O.31 FE2.12: 5 residues within 4Å: Chain E: K.48, H.51, H.63 Chain G: D.78, E.82 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:D.78, G:E.82, E:H.51, H2O.19, H2O.27 FE2.14: 5 residues within 4Å: Chain F: K.48, H.51, H.63 Chain H: D.78, E.82 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: H:D.78, H:E.82, F:H.51, H2O.22, H2O.22 FE2.16: 5 residues within 4Å: Chain I: D.78, E.82 Chain K: K.48, H.51, H.63 5 PLIP interactions: 1 interactions with chain K, 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: K:H.51, I:D.78, I:E.82, H2O.44, H2O.45 FE2.18: 4 residues within 4Å: Chain J: D.78, E.82 Chain L: K.48, H.51 5 PLIP interactions: 1 interactions with chain L, 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: L:H.51, J:D.78, J:E.82, H2O.41, H2O.47 FE2.20: 4 residues within 4Å: Chain I: H.51, H.63 Chain K: D.78, E.82 5 PLIP interactions: 1 interactions with chain I, 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: I:H.51, K:D.78, K:E.82, H2O.37, H2O.37 FE2.22: 4 residues within 4Å: Chain J: K.48, H.51 Chain L: D.78, E.82 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: L:D.78, L:E.82, J:H.51, H2O.39, H2O.50

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

SO4.4: 4 residues within 4Å: Chain A: R.70, T.74 Chain C: R.70, T.74 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.74 Salt bridges: C:R.70, A:R.70 SO4.6: 4 residues within 4Å: Chain B: R.70, T.74 Chain D: R.70, T.74 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:T.74, D:T.74 Salt bridges: B:R.70, D:R.70 SO4.9: 5 residues within 4Å: Chain E: R.70, T.71, T.74 Chain G: R.70, T.74 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain G Hydrogen bonds: E:T.74, E:T.74 Water bridges: E:T.71 Salt bridges: E:R.70, G:R.70 SO4.11: 4 residues within 4Å: Chain F: R.70, T.74 Chain H: R.70, T.74 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain H Hydrogen bonds: F:T.74, H:T.74 Salt bridges: F:R.70, H:R.70 SO4.19: 4 residues within 4Å: Chain J: R.70, T.74 Chain L: R.70, T.74 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain J Hydrogen bonds: L:T.74 Salt bridges: L:R.70, J:R.70 Water bridges: J:T.74 SO4.21: 4 residues within 4Å: Chain I: R.70, T.74 Chain K: R.70, T.74 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain K Hydrogen bonds: I:T.74, K:T.74 Salt bridges: I:R.70, K:R.70

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain D: D.146 Chain F: D.146 Chain K: D.146 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain B: D.146 Chain G: D.146 Chain L: D.146 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain C: D.146 Chain H: D.146 Chain J: D.146 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: D.146 Chain E: D.146 Chain I: D.146 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyamoto, T. et al., Structures of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis. Acta Crystallogr.,Sect.F (2011)

Release Date

2011-01-12

Peptides

DNA protection during starvation protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

DNA protection during starvation protein

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