SMTL ID : 2bw1.1

Iron-bound crystal structure of Dps-like peroxide resistance protein (Dpr) from Streptococcus suis.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-12-mer

Ligands

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 7 residues within 4Å: Chain C: R.46, G.47 Chain E: R.46, G.47, I.50 Chain L: R.46, G.47 6 PLIP interactions: 2 interactions with chain L, 1 interactions with chain E, 3 interactions with chain C Water bridges: L:R.46, L:G.47, E:G.47, C:R.46, C:G.47, C:E.158 EPE.3: 5 residues within 4Å: Chain D: R.46, G.47 Chain G: G.47 Chain I: R.46, G.47 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain D Water bridges: I:R.46, I:G.47, D:R.46, D:G.47, D:E.158 EPE.5: 5 residues within 4Å: Chain B: G.47 Chain F: R.46, G.47 Chain J: R.46, G.47 7 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B, 1 interactions with chain J Water bridges: F:R.46, F:G.47, F:G.47, F:E.158, F:E.158, B:G.47, J:G.47 EPE.7: 6 residues within 4Å: Chain A: R.46, G.47 Chain H: R.46, G.47 Chain K: R.46, G.47 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain K, 4 interactions with chain H Water bridges: A:G.47, K:G.47, H:R.46, H:R.46, H:G.47, H:E.158

12 x FE: FE (III) ION(Non-covalent)

FE.2: 3 residues within 4Å: Chain A: H.40 Chain C: D.67, E.71 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.67, C:E.71, A:H.40, H2O.2, H2O.13 FE.4: 3 residues within 4Å: Chain B: H.40 Chain D: D.67, E.71 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:D.67, D:D.67, D:E.71, B:H.40, H2O.7 FE.6: 3 residues within 4Å: Chain A: D.67, E.71 Chain C: H.40 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.40, A:D.67, A:E.71, H2O.12, H2O.12 FE.8: 3 residues within 4Å: Chain B: D.67, E.71 Chain D: H.40 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.67, B:E.71, D:H.40, H2O.17, H2O.17 FE.9: 3 residues within 4Å: Chain E: H.40 Chain G: D.67, E.71 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: E:H.40, G:D.67, G:D.67, H2O.23, H2O.33 FE.10: 3 residues within 4Å: Chain F: H.40 Chain H: D.67, E.71 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: F:H.40, H:D.67, H:E.71, H2O.28 FE.11: 3 residues within 4Å: Chain E: D.67, E.71 Chain G: H.40 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: E:D.67, E:D.67, E:E.71, G:H.40, H2O.24 FE.12: 3 residues within 4Å: Chain F: D.67, E.71 Chain H: H.40 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: F:D.67, F:D.67, F:E.71, H:H.40, H2O.37 FE.13: 3 residues within 4Å: Chain I: H.40 Chain K: D.67, E.71 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: K:D.67, K:D.67, K:E.71, I:H.40, H2O.41 FE.14: 3 residues within 4Å: Chain J: H.40 Chain L: D.67, E.71 5 PLIP interactions: 3 interactions with chain L, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: L:D.67, L:D.67, L:E.71, J:H.40, H2O.46 FE.16: 3 residues within 4Å: Chain I: D.67, E.71 Chain K: H.40 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: I:D.67, I:E.71, K:H.40, H2O.42, H2O.42 FE.17: 3 residues within 4Å: Chain J: D.67, E.71 Chain L: H.40 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: J:D.67, J:D.67, J:E.71, L:H.40, H2O.46

1 x CA: CALCIUM ION(Non-covalent)

CA.15: 2 residues within 4Å: Chain K: D.17, E.132 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.17, K:E.132, H2O.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kauko, A. et al., Iron incorporation in Streptococcus suis Dps-like peroxide resistance protein Dpr requires mobility in the ferroxidase center and leads to the formation of a ferrihydrite-like core. J. Mol. Biol. (2006)

Release Date

2006-09-27

Peptides

DPS-LIKE PEROXIDE RESISTANCE 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

DPS-LIKE PEROXIDE RESISTANCE PROTEIN

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