SMTL ID : 1jre.1

DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-12-mer

Ligands

13 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: E.82 Chain B: H.51, H.63, D.67 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.82, B:H.51, H2O.1, H2O.1, H2O.2 CD.4: 4 residues within 4Å: Chain A: H.51, H.63, D.67 Chain B: E.82 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.51, B:E.82, H2O.1, H2O.1, H2O.1 CD.7: 4 residues within 4Å: Chain C: E.82 Chain D: H.51, H.63, D.67 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:E.82, D:H.51, H2O.3 CD.10: 4 residues within 4Å: Chain C: H.51, H.63, D.67 Chain D: E.82 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:H.51, D:E.82, H2O.3, H2O.3 CD.14: 4 residues within 4Å: Chain E: E.82 Chain F: H.51, H.63, D.67 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: F:H.51, E:E.82, H2O.5, H2O.5 CD.16: 3 residues within 4Å: Chain E: H.51, D.67 Chain F: E.82 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: E:H.51, F:E.82, H2O.4, H2O.4, H2O.4 CD.17: 1 residues within 4Å: Chain G: E.120 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.120, G:E.120, H2O.5, H2O.5 CD.18: 3 residues within 4Å: Chain G: E.82 Chain H: H.51, D.67 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: H:H.51, G:E.82, H2O.6, H2O.7, H2O.7 CD.19: 3 residues within 4Å: Chain G: H.51, D.67 Chain H: E.82 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: G:H.51, H:E.82, H2O.5, H2O.5 CD.21: 4 residues within 4Å: Chain I: E.82 Chain J: H.51, H.63, D.67 5 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J, 3 Ligand-Water interactions Metal complexes: I:E.82, J:H.51, H2O.7, H2O.7, H2O.7 CD.22: 4 residues within 4Å: Chain I: H.51, H.63, D.67 Chain J: E.82 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: J:E.82, I:H.51, H2O.7, H2O.7, H2O.7 CD.23: 4 residues within 4Å: Chain K: E.82 Chain L: H.51, H.63, D.67 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L, 3 Ligand-Water interactions Metal complexes: K:E.82, L:H.51, H2O.8, H2O.8, H2O.8 CD.25: 4 residues within 4Å: Chain K: H.51, H.63, D.67 Chain L: E.82 5 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: L:E.82, K:H.51, H2O.8, H2O.8, H2O.9

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

TRS.2: 3 residues within 4Å: Chain A: D.146 Chain E: D.146 Chain I: D.146 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain I Hydrogen bonds: E:R.153, I:D.146, I:R.153 TRS.3: 6 residues within 4Å: Chain A: A.57, E.167 Chain H: A.57, E.167 Chain J: A.57, E.167 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain H, 2 interactions with chain J Hydrogen bonds: A:E.167, H:E.167, J:E.167, J:E.167 TRS.5: 4 residues within 4Å: Chain B: D.146 Chain H: D.146, R.153 Chain K: D.146 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain H Hydrogen bonds: B:D.146, B:R.153, H:R.153 Water bridges: H:R.153 TRS.6: 5 residues within 4Å: Chain B: A.57, E.167 Chain E: A.57, E.167 Chain L: E.167 4 PLIP interactions: 2 interactions with chain L, 1 interactions with chain E, 1 interactions with chain B Hydrogen bonds: L:E.167, E:E.167, B:E.167 Water bridges: L:E.167 TRS.8: 6 residues within 4Å: Chain C: A.57, E.167 Chain G: A.57, E.167 Chain K: A.57, E.167 4 PLIP interactions: 2 interactions with chain K, 1 interactions with chain G, 1 interactions with chain C Hydrogen bonds: K:E.167, K:E.167, G:E.167, C:E.167 TRS.9: 3 residues within 4Å: Chain C: D.146 Chain F: D.146 Chain L: D.146 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.146 TRS.11: 3 residues within 4Å: Chain D: E.64 Chain F: E.64 Chain I: E.64 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain I Hydrogen bonds: D:E.64, I:E.64 TRS.12: 6 residues within 4Å: Chain D: A.57, E.167 Chain F: A.57, E.167 Chain I: A.57, E.167 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 interactions with chain I Hydrogen bonds: F:E.167, D:E.167, I:E.167 TRS.13: 5 residues within 4Å: Chain D: D.146, R.153 Chain G: D.146, R.153 Chain J: D.146 4 PLIP interactions: 2 interactions with chain J, 1 interactions with chain D, 1 interactions with chain G Hydrogen bonds: J:D.146, J:R.153, D:R.153, G:R.153 TRS.15: 3 residues within 4Å: Chain B: E.64 Chain E: E.64 Chain L: E.64 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.64 TRS.20: 3 residues within 4Å: Chain A: E.64 Chain H: E.64 Chain J: E.64 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:E.64, A:E.64 TRS.24: 3 residues within 4Å: Chain C: E.64 Chain G: E.64 Chain K: E.64 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain C, 1 interactions with chain K Hydrogen bonds: G:E.64, G:E.64, K:E.64 Water bridges: C:E.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, J. et al., DNA Protection and Binding by E. Coli Dps Protein. To be Published

Release Date

2003-06-17

Peptides

DNA PROTECTION DURING STARVATION 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

DNA PROTECTION DURING STARVATION PROTEIN

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