SMTL ID : 1vel.1

Mycobacterium smegmatis Dps tetragonal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

homo-12-mer

Ligands

20 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: H.39 Chain G: D.66, E.70 Ligand excluded by PLIP CD.2: 3 residues within 4Å: Chain A: D.136 Chain B: D.136 Chain C: D.136 Ligand excluded by PLIP CD.5: 4 residues within 4Å: Chain B: K.36, H.39 Chain J: D.66, E.70 Ligand excluded by PLIP CD.6: 4 residues within 4Å: Chain C: D.66, E.70 Chain E: H.39, H.51 Ligand excluded by PLIP CD.7: 1 residues within 4Å: Chain C: E.118 Ligand excluded by PLIP CD.8: 4 residues within 4Å: Chain D: H.39, H.51 Chain H: D.66, E.70 Ligand excluded by PLIP CD.9: 3 residues within 4Å: Chain D: D.136 Chain E: D.136 Chain F: D.136 Ligand excluded by PLIP CD.10: 1 residues within 4Å: Chain D: D.129 Ligand excluded by PLIP CD.13: 4 residues within 4Å: Chain C: K.36, H.39 Chain E: D.66, E.70 Ligand excluded by PLIP CD.14: 4 residues within 4Å: Chain F: K.36, H.39 Chain L: D.66, E.70 Ligand excluded by PLIP CD.15: 3 residues within 4Å: Chain A: D.66, E.70 Chain G: H.39 Ligand excluded by PLIP CD.16: 3 residues within 4Å: Chain G: D.136 Chain H: D.136 Chain I: D.136 Ligand excluded by PLIP CD.19: 4 residues within 4Å: Chain D: D.66, E.70 Chain H: K.36, H.39 Ligand excluded by PLIP CD.20: 4 residues within 4Å: Chain I: D.66, E.70 Chain K: H.39, H.51 Ligand excluded by PLIP CD.21: 1 residues within 4Å: Chain I: E.118 Ligand excluded by PLIP CD.22: 4 residues within 4Å: Chain B: D.66, E.70 Chain J: H.39, H.51 Ligand excluded by PLIP CD.23: 3 residues within 4Å: Chain J: D.136 Chain K: D.136 Chain L: D.136 Ligand excluded by PLIP CD.24: 1 residues within 4Å: Chain J: D.129 Ligand excluded by PLIP CD.27: 4 residues within 4Å: Chain I: K.36, H.39 Chain K: D.66, E.70 Ligand excluded by PLIP CD.28: 4 residues within 4Å: Chain F: D.66, E.70 Chain L: K.36, H.39 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: E.128 Chain B: E.128 Chain C: E.128 Ligands: SO4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.128 NA.11: 3 residues within 4Å: Chain D: E.128 Chain E: E.128 Ligands: SO4.12 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.128 NA.17: 4 residues within 4Å: Chain G: E.128 Chain H: E.128 Chain I: E.128 Ligands: SO4.18 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:E.128 NA.25: 3 residues within 4Å: Chain J: E.128 Chain K: E.128 Ligands: SO4.26 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:E.128

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain A: Q.135, I.139 Chain B: Q.135 Chain C: Q.135, I.139 Ligands: NA.3 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Q.135, C:Q.135, A:Q.135 SO4.12: 6 residues within 4Å: Chain D: Q.135, I.139 Chain E: Q.135 Chain F: Q.135, I.139 Ligands: NA.11 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: E:Q.135, D:Q.135, D:D.136, F:Q.135 SO4.18: 6 residues within 4Å: Chain G: Q.135, I.139 Chain H: Q.135 Chain I: Q.135, I.139 Ligands: NA.17 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G, 1 interactions with chain I Hydrogen bonds: H:Q.135, G:Q.135, I:Q.135 SO4.26: 6 residues within 4Å: Chain J: Q.135, I.139 Chain K: Q.135 Chain L: Q.135, I.139 Ligands: NA.25 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K, 1 interactions with chain L Hydrogen bonds: J:Q.135, K:Q.135, L:Q.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roy, S. et al., X-ray analysis of Mycobacterium smegmatis Dps and a comparative study involving other Dps and Dps-like molecules. J.Mol.Biol. (2004)

Release Date

2004-06-29

Peptides

starvation-induced DNA protecting protein: 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

starvation-induced DNA protecting protein

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