SMTL ID : 1o9r.1

The X-ray crystal structure of Agrobacterium tumefaciens Dps, a member of the family that protect DNA without binding

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-12-mer

Ligands

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

FE.1: 2 residues within 4Å: Chain A: E.71 Chain B: H.40 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.71, H2O.7, H2O.7 FE.2: 2 residues within 4Å: Chain A: H.40 Chain B: E.71 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.71, H2O.2, H2O.2 FE.4: 2 residues within 4Å: Chain C: E.71 Chain I: H.40 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: C:E.71, I:H.40, H2O.40, H2O.41 FE.5: 2 residues within 4Å: Chain D: E.71 Chain J: H.40 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.71, H2O.17, H2O.45 FE.7: 2 residues within 4Å: Chain E: E.71 Chain F: H.40 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: E:E.71, F:H.40, H2O.22, H2O.25, H2O.26 FE.9: 2 residues within 4Å: Chain E: H.40 Chain F: E.71 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: E:H.40, F:E.71, H2O.21, H2O.21, H2O.26 FE.10: 2 residues within 4Å: Chain G: E.71 Chain H: H.40 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.71, H2O.35, H2O.36 FE.11: 2 residues within 4Å: Chain G: H.40 Chain H: E.71 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.71, H2O.31, H2O.31 FE.13: 2 residues within 4Å: Chain C: H.40 Chain I: E.71 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: I:E.71, C:H.40, H2O.12, H2O.12 FE.14: 2 residues within 4Å: Chain D: H.40 Chain J: E.71 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.71, H2O.17, H2O.46 FE.16: 2 residues within 4Å: Chain K: E.71 Chain L: H.40 5 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: L:H.40, K:E.71, H2O.50, H2O.54, H2O.54 FE.18: 2 residues within 4Å: Chain K: H.40 Chain L: E.71 5 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: L:E.71, K:H.40, H2O.49, H2O.50, H2O.55

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 6 residues within 4Å: Chain B: D.138, R.145 Chain D: D.138, R.145 Chain L: D.138, R.145 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain L, 1 interactions with chain D Hydrogen bonds: B:R.145, L:D.138, L:R.145, D:R.145 TRS.8: 6 residues within 4Å: Chain A: D.138, R.145 Chain C: D.138, R.145 Chain E: D.138, R.145 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: C:D.138, C:R.145, A:R.145, E:R.145 TRS.12: 6 residues within 4Å: Chain F: D.138, R.145 Chain H: D.138, R.145 Chain J: D.138, R.145 4 PLIP interactions: 1 interactions with chain J, 2 interactions with chain F, 1 interactions with chain H Hydrogen bonds: J:R.145, F:D.138, F:R.145, H:R.145 TRS.17: 6 residues within 4Å: Chain G: D.138, R.145 Chain I: D.138, R.145 Chain K: D.138, R.145 4 PLIP interactions: 2 interactions with chain I, 1 interactions with chain K, 1 interactions with chain G Hydrogen bonds: I:D.138, I:R.145, K:R.145, G:R.145

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 8 residues within 4Å: Chain D: I.30, A.33, L.62, D.63, G.66, D.67 Chain J: W.41, R.59 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain J Hydrogen bonds: D:D.67, J:R.59 Water bridges: D:R.59, J:R.59, J:R.59 EDO.15: 8 residues within 4Å: Chain D: W.41, R.59 Chain J: I.30, A.33, L.62, D.63, G.66, D.67 5 PLIP interactions: 2 interactions with chain J, 3 interactions with chain D Hydrogen bonds: J:D.67, D:R.59 Water bridges: J:R.59, D:R.59, D:R.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ceci, P. et al., The Dps Protein of Agrobacterium Tumefaciens Does not Bind to DNA But Protects It Toward Oxidative Cleavage: X-Ray Crystal Structure, Iron Binding, and Hydroxyl-Radical Scavenging Properties. J.Biol.Chem. (2003)

Release Date

2003-05-29

Peptides

AGROBACTERIUM TUMEFACIENS DPS: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

AGROBACTERIUM TUMEFACIENS DPS