SMTL ID : 1umn.1

Crystal structure of Dps-like peroxide resistance protein (Dpr) from Streptococcus suis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-12-mer

Ligands

16 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 1 residues within 4Å: Chain A: D.56 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.56, H2O.2, H2O.2, H2O.14, H2O.14 CA.2: 1 residues within 4Å: Chain B: D.56 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.56, H2O.8, H2O.20, H2O.20, H2O.20 CA.3: 1 residues within 4Å: Chain C: D.56 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.56, H2O.1, H2O.3, H2O.3, H2O.14 CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 1 residues within 4Å: Chain D: D.56 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.56, H2O.7, H2O.9, H2O.19, H2O.19 CA.8: 1 residues within 4Å: Chain E: D.56 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.56, H2O.25, H2O.26, H2O.37, H2O.37 CA.9: 1 residues within 4Å: Chain F: D.56 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.56, H2O.30, H2O.31, H2O.41, H2O.42 CA.10: 1 residues within 4Å: Chain G: N.101 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:N.101, H2O.38, H2O.38 CA.11: 1 residues within 4Å: Chain G: D.56 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:D.56, H2O.25, H2O.26, H2O.36, H2O.36 CA.13: 1 residues within 4Å: Chain H: D.56 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:D.56, H2O.31, H2O.32, H2O.41, H2O.41 CA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.17: 1 residues within 4Å: Chain I: D.56 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.46, H2O.47, H2O.47, H2O.57, H2O.57 CA.19: 1 residues within 4Å: Chain J: D.56 5 PLIP interactions: 1 interactions with chain J, 4 Ligand-Water interactions Metal complexes: J:D.56, H2O.51, H2O.52, H2O.52, H2O.62 CA.21: 2 residues within 4Å: Chain K: D.17, E.132 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.17, K:E.132 CA.22: 1 residues within 4Å: Chain K: D.56 5 PLIP interactions: 1 interactions with chain K, 4 Ligand-Water interactions Metal complexes: K:D.56, H2O.47, H2O.47, H2O.57, H2O.57 CA.23: 2 residues within 4Å: Chain L: D.56, E.60 5 PLIP interactions: 1 interactions with chain L, 4 Ligand-Water interactions Metal complexes: L:D.56, H2O.52, H2O.52, H2O.62, H2O.62

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain D: T.103, I.104 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain H: R.44, G.45, T.103, I.104 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain I: R.44, G.45, T.103, I.104 Ligand excluded by PLIP

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

EPE.7: 7 residues within 4Å: Chain C: R.46, G.47 Chain E: R.46, G.47 Chain L: R.46, G.47, I.50 6 PLIP interactions: 4 interactions with chain L, 1 interactions with chain C, 1 interactions with chain E Water bridges: L:R.46, L:G.47, L:G.47, L:E.158, C:R.46, E:G.47 EPE.14: 7 residues within 4Å: Chain D: R.46, G.47 Chain G: R.46, G.47 Chain I: R.46, G.47, I.50 6 PLIP interactions: 3 interactions with chain I, 2 interactions with chain D, 1 interactions with chain G Water bridges: I:R.46, I:G.47, I:E.158, D:R.46, D:G.47, G:G.47 EPE.18: 7 residues within 4Å: Chain B: G.47, I.50 Chain F: R.46, G.47 Chain J: R.46, G.47, I.50 7 PLIP interactions: 4 interactions with chain F, 2 interactions with chain B, 1 interactions with chain J Water bridges: F:R.46, F:G.47, F:G.47, F:E.158, B:R.46, B:G.47, J:G.47 EPE.20: 5 residues within 4Å: Chain A: G.47 Chain H: R.46, G.47 Chain K: R.46, G.47 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain K, 2 interactions with chain H Water bridges: A:R.46, A:G.47, A:E.158, K:G.47, H:R.46, H:G.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kauko, A. et al., Crystal structure of Streptococcus suis Dps-like peroxide resistance protein Dpr: implications for iron incorporation. J. Mol. Biol. (2004)

Release Date

2004-04-23

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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