SMTL ID : 6hvq.1

The structure of Dps from Listeria innocua soaked before soaking experiments with Zn, Co and La

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-10-2-mer

Ligands

100 x LA: LANTHANUM (III) ION(Non-covalent)(Non-functional Binders)

LA.1: 3 residues within 4Å: Chain A: D.130 Chain C: D.130 Chain E: D.130 Ligand excluded by PLIP LA.2: 4 residues within 4Å: Chain A: D.58, E.62 Chain B: H.31 Chain C: K.141 Ligand excluded by PLIP LA.3: 4 residues within 4Å: Chain A: N.5, S.6, V.7, E.11 Ligand excluded by PLIP LA.4: 2 residues within 4Å: Chain A: E.118 Ligands: LA.5 Ligand excluded by PLIP LA.5: 3 residues within 4Å: Chain A: D.121 Ligands: LA.4, LA.38 Ligand excluded by PLIP LA.6: 3 residues within 4Å: Chain A: E.44 Ligands: LA.31, LA.45 Ligand excluded by PLIP LA.7: 4 residues within 4Å: Chain A: D.121 Chain C: D.121 Ligands: LA.23, LA.24 Ligand excluded by PLIP LA.8: 2 residues within 4Å: Chain A: D.58 Ligands: LA.9 Ligand excluded by PLIP LA.9: 1 residues within 4Å: Ligands: LA.8 Ligand excluded by PLIP LA.10: 3 residues within 4Å: Chain A: H.31 Chain B: D.58, E.62 Ligand excluded by PLIP LA.11: 3 residues within 4Å: Chain B: S.6, V.7, E.11 Ligand excluded by PLIP LA.12: 2 residues within 4Å: Chain B: H.37 Chain C: D.96 Ligand excluded by PLIP LA.13: 3 residues within 4Å: Chain B: E.44 Ligands: LA.14, LA.22 Ligand excluded by PLIP LA.14: 3 residues within 4Å: Chain K: E.44 Ligands: LA.13, LA.22 Ligand excluded by PLIP LA.15: 4 residues within 4Å: Chain B: E.55, D.58, E.59 Ligands: LA.17 Ligand excluded by PLIP LA.16: 3 residues within 4Å: Chain B: E.55, E.59 Ligands: LA.17 Ligand excluded by PLIP LA.17: 3 residues within 4Å: Chain B: E.59 Ligands: LA.15, LA.16 Ligand excluded by PLIP LA.18: 4 residues within 4Å: Chain C: D.58, E.62 Chain E: K.141 Chain I: H.31 Ligand excluded by PLIP LA.19: 1 residues within 4Å: Chain C: E.100 Ligand excluded by PLIP LA.20: 2 residues within 4Å: Chain C: E.118 Ligands: LA.23 Ligand excluded by PLIP LA.21: 3 residues within 4Å: Chain C: S.6, V.7, E.11 Ligand excluded by PLIP LA.22: 3 residues within 4Å: Chain C: E.44 Ligands: LA.13, LA.14 Ligand excluded by PLIP LA.23: 3 residues within 4Å: Chain C: D.121 Ligands: LA.7, LA.20 Ligand excluded by PLIP LA.24: 3 residues within 4Å: Chain C: D.121 Ligands: LA.7, LA.37 Ligand excluded by PLIP LA.25: 3 residues within 4Å: Chain C: D.58, E.59 Ligands: LA.26 Ligand excluded by PLIP LA.26: 2 residues within 4Å: Chain C: E.59 Ligands: LA.25 Ligand excluded by PLIP LA.27: 4 residues within 4Å: Chain D: D.58, E.62 Chain J: H.31 Chain L: K.141 Ligand excluded by PLIP LA.28: 1 residues within 4Å: Chain D: E.118 Ligand excluded by PLIP LA.29: 3 residues within 4Å: Chain D: S.6, V.7, E.11 Ligand excluded by PLIP LA.30: 3 residues within 4Å: Chain D: D.96, E.100 Ligands: LA.32 Ligand excluded by PLIP LA.31: 3 residues within 4Å: Chain D: E.44 Ligands: LA.6, LA.45 Ligand excluded by PLIP LA.32: 2 residues within 4Å: Chain D: E.100 Ligands: LA.30 Ligand excluded by PLIP LA.33: 1 residues within 4Å: Chain D: E.85 Ligand excluded by PLIP LA.34: 1 residues within 4Å: Chain D: E.85 Ligand excluded by PLIP LA.35: 3 residues within 4Å: Chain E: D.58, E.62 Chain F: H.31 Ligand excluded by PLIP LA.36: 2 residues within 4Å: Chain E: E.118 Ligands: LA.37 Ligand excluded by PLIP LA.37: 3 residues within 4Å: Chain E: D.121 Ligands: LA.24, LA.36 Ligand excluded by PLIP LA.38: 2 residues within 4Å: Chain E: D.121 Ligands: LA.5 Ligand excluded by PLIP LA.39: 1 residues within 4Å: Chain E: D.58 Ligand excluded by PLIP LA.40: 1 residues within 4Å: Chain E: E.85 Ligand excluded by PLIP LA.41: 3 residues within 4Å: Chain E: H.31 Chain F: D.58, E.62 Ligand excluded by PLIP LA.42: 3 residues within 4Å: Chain F: D.130 Chain H: D.130 Chain J: D.130 Ligand excluded by PLIP LA.43: 1 residues within 4Å: Chain F: D.121 Ligand excluded by PLIP LA.44: 3 residues within 4Å: Chain F: S.6, V.7, E.11 Ligand excluded by PLIP LA.45: 3 residues within 4Å: Chain F: E.44 Ligands: LA.6, LA.31 Ligand excluded by PLIP LA.46: 2 residues within 4Å: Chain J: D.58, E.59 Ligand excluded by PLIP LA.47: 1 residues within 4Å: Chain F: E.85 Ligand excluded by PLIP LA.48: 2 residues within 4Å: Chain F: D.58 Ligands: LA.50 Ligand excluded by PLIP LA.49: 1 residues within 4Å: Chain F: D.111 Ligand excluded by PLIP LA.50: 1 residues within 4Å: Ligands: LA.48 Ligand excluded by PLIP LA.51: 3 residues within 4Å: Chain G: D.130 Chain I: D.130 Chain K: D.130 Ligand excluded by PLIP LA.52: 4 residues within 4Å: Chain G: D.58, E.62 Chain H: H.31 Chain I: K.141 Ligand excluded by PLIP LA.53: 4 residues within 4Å: Chain G: N.5, S.6, V.7, E.11 Ligand excluded by PLIP LA.54: 2 residues within 4Å: Chain G: E.118 Ligands: LA.55 Ligand excluded by PLIP LA.55: 3 residues within 4Å: Chain G: D.121 Ligands: LA.54, LA.88 Ligand excluded by PLIP LA.56: 3 residues within 4Å: Chain G: E.44 Ligands: LA.81, LA.95 Ligand excluded by PLIP LA.57: 4 residues within 4Å: Chain G: D.121 Chain I: D.121 Ligands: LA.73, LA.74 Ligand excluded by PLIP LA.58: 2 residues within 4Å: Chain G: D.58 Ligands: LA.59 Ligand excluded by PLIP LA.59: 1 residues within 4Å: Ligands: LA.58 Ligand excluded by PLIP LA.60: 3 residues within 4Å: Chain G: H.31 Chain H: D.58, E.62 Ligand excluded by PLIP LA.61: 3 residues within 4Å: Chain H: S.6, V.7, E.11 Ligand excluded by PLIP LA.62: 2 residues within 4Å: Chain H: H.37 Chain I: D.96 Ligand excluded by PLIP LA.63: 3 residues within 4Å: Chain H: E.44 Ligands: LA.64, LA.72 Ligand excluded by PLIP LA.64: 3 residues within 4Å: Chain E: E.44 Ligands: LA.63, LA.72 Ligand excluded by PLIP LA.65: 4 residues within 4Å: Chain H: E.55, D.58, E.59 Ligands: LA.67 Ligand excluded by PLIP LA.66: 3 residues within 4Å: Chain H: E.55, E.59 Ligands: LA.67 Ligand excluded by PLIP LA.67: 3 residues within 4Å: Chain H: E.59 Ligands: LA.65, LA.66 Ligand excluded by PLIP LA.68: 4 residues within 4Å: Chain C: H.31 Chain I: D.58, E.62 Chain K: K.141 Ligand excluded by PLIP LA.69: 1 residues within 4Å: Chain I: E.100 Ligand excluded by PLIP LA.70: 2 residues within 4Å: Chain I: E.118 Ligands: LA.73 Ligand excluded by PLIP LA.71: 3 residues within 4Å: Chain I: S.6, V.7, E.11 Ligand excluded by PLIP LA.72: 3 residues within 4Å: Chain I: E.44 Ligands: LA.63, LA.64 Ligand excluded by PLIP LA.73: 3 residues within 4Å: Chain I: D.121 Ligands: LA.57, LA.70 Ligand excluded by PLIP LA.74: 3 residues within 4Å: Chain I: D.121 Ligands: LA.57, LA.87 Ligand excluded by PLIP LA.75: 3 residues within 4Å: Chain I: D.58, E.59 Ligands: LA.76 Ligand excluded by PLIP LA.76: 2 residues within 4Å: Chain I: E.59 Ligands: LA.75 Ligand excluded by PLIP LA.77: 4 residues within 4Å: Chain D: H.31 Chain F: K.141 Chain J: D.58, E.62 Ligand excluded by PLIP LA.78: 1 residues within 4Å: Chain J: E.118 Ligand excluded by PLIP LA.79: 3 residues within 4Å: Chain J: S.6, V.7, E.11 Ligand excluded by PLIP LA.80: 3 residues within 4Å: Chain J: D.96, E.100 Ligands: LA.82 Ligand excluded by PLIP LA.81: 3 residues within 4Å: Chain J: E.44 Ligands: LA.56, LA.95 Ligand excluded by PLIP LA.82: 2 residues within 4Å: Chain J: E.100 Ligands: LA.80 Ligand excluded by PLIP LA.83: 1 residues within 4Å: Chain J: E.85 Ligand excluded by PLIP LA.84: 1 residues within 4Å: Chain J: E.85 Ligand excluded by PLIP LA.85: 3 residues within 4Å: Chain K: D.58, E.62 Chain L: H.31 Ligand excluded by PLIP LA.86: 2 residues within 4Å: Chain K: E.118 Ligands: LA.87 Ligand excluded by PLIP LA.87: 3 residues within 4Å: Chain K: D.121 Ligands: LA.74, LA.86 Ligand excluded by PLIP LA.88: 2 residues within 4Å: Chain K: D.121 Ligands: LA.55 Ligand excluded by PLIP LA.89: 1 residues within 4Å: Chain K: D.58 Ligand excluded by PLIP LA.90: 1 residues within 4Å: Chain K: E.85 Ligand excluded by PLIP LA.91: 3 residues within 4Å: Chain K: H.31 Chain L: D.58, E.62 Ligand excluded by PLIP LA.92: 3 residues within 4Å: Chain B: D.130 Chain D: D.130 Chain L: D.130 Ligand excluded by PLIP LA.93: 1 residues within 4Å: Chain L: D.121 Ligand excluded by PLIP LA.94: 3 residues within 4Å: Chain L: S.6, V.7, E.11 Ligand excluded by PLIP LA.95: 3 residues within 4Å: Chain L: E.44 Ligands: LA.56, LA.81 Ligand excluded by PLIP LA.96: 2 residues within 4Å: Chain D: D.58, E.59 Ligand excluded by PLIP LA.97: 1 residues within 4Å: Chain L: E.85 Ligand excluded by PLIP LA.98: 2 residues within 4Å: Chain L: D.58 Ligands: LA.100 Ligand excluded by PLIP LA.99: 1 residues within 4Å: Chain L: D.111 Ligand excluded by PLIP LA.100: 1 residues within 4Å: Ligands: LA.98 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeth, K. et al., Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps. Inorg.Chem. (2019)

Release Date

2019-09-04

Peptides

DNA protection during starvation protein: ABCDFGHIJL
DNA protection during starvation protein: EK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

G
A

H
B

I
C

J
D

L
F

E
E

K
E

DNA protection during starvation protein

DNA protection during starvation protein

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