SMTL ID : 2yjk.1

Structure of Dps from MICROBACTERIUM ARBORESCENS in the high iron form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-12-mer

Ligands

11 x OFE: Iron(II) oxide(Non-covalent)

OFE.1: 5 residues within 4Å: Chain A: D.70, E.74 Chain B: K.40, H.43, D.59 6 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:H.43, A:D.70, A:E.74, OFE.1, H2O.2 Hydrogen bonds: A:D.70 OFE.2: 5 residues within 4Å: Chain A: K.40, H.43, D.59 Chain B: D.70, E.74 7 PLIP interactions: 3 interactions with chain B, 3 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 Water bridges: A:K.40 OFE.4: 5 residues within 4Å: Chain C: D.70, E.74 Chain I: K.40, H.43, D.59 5 PLIP interactions: 1 interactions with chain I, 2 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: I:H.43, C:D.70, C:E.74, OFE.4, H2O.6 OFE.6: 5 residues within 4Å: Chain D: D.70, E.74 Chain J: K.40, H.43, D.59 7 PLIP interactions: 2 interactions with chain J, 3 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrogen bonds: J:K.40, D:D.70 Metal complexes: J:H.43, D:D.70, D:E.74, OFE.6, H2O.8 OFE.8: 5 residues within 4Å: Chain E: D.70, E.74 Chain F: K.40, H.43, D.59 7 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrogen bonds: F:K.40 Water bridges: F:K.40 Metal complexes: F:H.43, E:D.70, E:E.74, OFE.8, H2O.10 OFE.9: 4 residues within 4Å: Chain E: H.43, H.55 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.9, H2O.10 Hydrogen bonds: E:H.55 OFE.10: 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.10, H2O.15 OFE.11: 5 residues within 4Å: Chain C: K.40, H.43, D.59 Chain I: D.70, E.74 6 PLIP interactions: 2 interactions with chain I, 2 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: I:D.70, I:E.74, C:H.43, H2O.5, OFE.11 Hydrogen bonds: C:H.43 OFE.13: 5 residues within 4Å: Chain D: K.40, H.43, D.59 Chain J: D.70, E.74 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain J, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Hydrogen bonds: D:D.59 Metal complexes: D:H.43, J:D.70, J:E.74, H2O.7, OFE.13 OFE.15: 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 K, 2 interactions with chain L, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: K:D.70, K:E.74, L:H.43, OFE.15, H2O.24 Hydrogen bonds: L:D.59 OFE.16: 5 residues within 4Å: Chain K: K.40, H.43, D.59 Chain L: D.70, E.74 6 PLIP interactions: 2 interactions with chain K, 3 interactions with chain L, 1 Ligand-Ligand interactions Hydrogen bonds: K:K.40 Metal complexes: K:H.43, L:D.70, L:D.70, L:E.74, OFE.16

6 x FE: FE (III) ION(Non-functional Binders)(Non-covalent)

FE.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE.7: 1 residues within 4Å: Chain G: D.131 No protein-ligand interaction detected (PLIP) FE.12: 3 residues within 4Å: Chain G: H.43 Chain H: D.70, E.74 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: H:D.70, H:D.70, H:E.74, G:H.43, H2O.15 FE.14: 1 residues within 4Å: Chain F: D.131 No protein-ligand interaction detected (PLIP) FE.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

2011-06-01

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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