SMTL ID : 2yjj.1

Structure of Dps from MICROBACTERIUM ARBORESCENS in the low iron form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-12-mer

Ligands

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

FE.1: 3 residues within 4Å: Chain A: D.70, E.74 Chain B: H.43 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:H.43, A:D.70, A:D.70, A:E.74 FE.12: 3 residues within 4Å: Chain K: H.43 Chain L: D.70, E.74 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L Metal complexes: K:H.43, L:D.70, L:D.70, L:E.74

10 x OFE: Iron(II) oxide(Non-covalent)(Covalent)

OFE.2: 5 residues within 4Å: Chain A: K.40, H.43, D.59 Chain B: D.70, E.74 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:D.70, B:D.70, B:E.74, A:H.43, OFE.2 Hydrogen bonds: A:D.59 OFE.3: 5 residues within 4Å: Chain C: D.70, E.74 Chain I: H.43, H.55, D.59 5 PLIP interactions: 1 interactions with chain I, 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: I:H.43, C:D.70, C:E.74, OFE.3 Hydrogen bonds: C:E.74 OFE.4: 5 residues within 4Å: Chain D: D.70, E.74 Chain J: K.40, H.43, D.59 6 PLIP interactions: 1 interactions with chain J, 3 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: J:H.43, D:D.70, D:E.74, OFE.4, H2O.11 Hydrogen bonds: D:D.70 OFE.5: 5 residues within 4Å: Chain E: K.40, H.43, D.59 Chain F: D.70, E.74 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: F:D.70, F:E.74, E:H.43, OFE.5, H2O.13 Hydrogen bonds: E:D.59 OFE.6: 5 residues within 4Å: Chain E: D.70, E.74 Chain F: K.40, H.43, D.59 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrogen bonds: F:D.59 Metal complexes: F:H.43, E:D.70, E:E.74, OFE.6, H2O.14 OFE.7: 5 residues within 4Å: Chain G: D.70, E.74 Chain H: K.40, H.43, D.59 6 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrogen bonds: H:D.59 Metal complexes: H:H.43, G:D.70, G:E.74, OFE.7, H2O.20 OFE.8: 4 residues within 4Å: Chain G: H.43, H.55 Chain H: D.70, E.74 6 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G, 1 Ligand-Ligand interactions Hydrogen bonds: H:E.74 Metal complexes: H:D.70, H:D.70, H:E.74, G:H.43, OFE.8 OFE.9: 5 residues within 4Å: Chain C: K.40, H.43, D.59 Chain I: D.70, E.74 7 PLIP interactions: 2 interactions with chain I, 3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: I:D.70, I:E.74, C:H.43, OFE.9, H2O.25 Hydrogen bonds: C:K.40 Water bridges: C:K.40 OFE.10: 5 residues within 4Å: Chain D: K.40, H.43, D.59 Chain J: D.70, E.74 7 PLIP interactions: 3 interactions with chain D, 2 interactions with chain J, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Hydrogen bonds: D:D.59 Water bridges: D:K.40 Metal complexes: D:H.43, J:D.70, J:E.74, H2O.10, OFE.10 OFE.11: 5 residues within 4Å: Chain K: D.70, E.74 Chain L: K.40, H.43, D.59 6 PLIP interactions: 2 interactions with chain L, 2 interactions with chain K, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrogen bonds: L:D.59 Metal complexes: L:H.43, K:D.70, K:E.74, OFE.11, H2O.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pesek, J. et al., Structure and Mechanism of Iron Translocation by a Dps Protein from Microbacterium Arborescens. J.Biol.Chem. (2011)

Release Date

2011-06-29

Peptides

AFP: 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

AFP

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