SMTL ID : 2z90.1

Crystal Structure of the Second Dps from Mycobacterium smegmatis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-12-mer

Ligands

12 x FE2: FE (II) ION(Non-covalent)

FE2.1: 5 residues within 4Å: Chain A: D.68, E.72 Chain B: K.38, H.41, D.57 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.68, A:D.68, A:E.72, B:H.41, H2O.4 FE2.4: 5 residues within 4Å: Chain A: K.38, H.41, D.57 Chain B: D.68, E.72 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.68, B:D.68, B:E.72, A:H.41, H2O.8 FE2.6: 5 residues within 4Å: Chain C: D.68, E.72 Chain D: K.38, H.41, D.57 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:D.68, C:D.68, C:E.72, D:H.41, H2O.12 FE2.7: 5 residues within 4Å: Chain C: K.38, H.41, D.57 Chain D: D.68, E.72 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Metal complexes: D:D.68, D:D.68, D:E.72, C:H.41 FE2.9: 5 residues within 4Å: Chain E: D.68, E.72 Chain F: K.38, H.41, D.57 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:D.68, E:D.68, E:E.72, F:H.41, H2O.19 FE2.12: 5 residues within 4Å: Chain E: K.38, H.41, D.57 Chain F: D.68, E.72 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:H.41, F:D.68, F:D.68, F:E.72, H2O.24 FE2.14: 5 residues within 4Å: Chain G: D.68, E.72 Chain H: K.38, H.41, D.57 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:D.68, G:D.68, G:E.72, H:H.41, H2O.28 FE2.15: 5 residues within 4Å: Chain G: K.38, H.41, D.57 Chain H: D.68, E.72 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G Metal complexes: H:D.68, H:D.68, H:E.72, G:H.41 FE2.17: 5 residues within 4Å: Chain I: D.68, E.72 Chain J: K.38, H.41, D.57 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: I:D.68, I:D.68, I:E.72, J:H.41, H2O.35 FE2.20: 5 residues within 4Å: Chain I: K.38, H.41, D.57 Chain J: D.68, E.72 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: J:D.68, J:D.68, J:E.72, I:H.41, H2O.40 FE2.22: 5 residues within 4Å: Chain K: D.68, E.72 Chain L: K.38, H.41, D.57 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: K:D.68, K:D.68, K:E.72, L:H.41, H2O.44 FE2.23: 5 residues within 4Å: Chain K: K.38, H.41, D.57 Chain L: D.68, E.72 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L Metal complexes: K:H.41, L:D.68, L:D.68, L:E.72

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: N.48, D.51 Chain E: N.48, D.51 Chain I: N.48, D.51 Ligands: MG.10, MG.18 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A, 1 interactions with chain E Metal complexes: I:D.51, A:D.51, E:D.51 MG.8: 6 residues within 4Å: Chain D: N.48, D.51 Chain F: N.48, D.51 Chain G: N.48, D.51 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 interactions with chain G Metal complexes: F:D.51, D:D.51, G:D.51 MG.10: 8 residues within 4Å: Chain A: N.48, D.51 Chain E: N.48, D.51 Chain I: N.48, D.51 Ligands: MG.2, MG.18 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A, 1 interactions with chain E Metal complexes: I:D.51, A:D.51, E:D.51 MG.16: 6 residues within 4Å: Chain H: N.48, D.51 Chain J: N.48, D.51 Chain K: N.48, D.51 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K, 1 interactions with chain H Metal complexes: J:D.51, K:D.51, H:D.51 MG.18: 8 residues within 4Å: Chain A: N.48, D.51 Chain E: N.48, D.51 Chain I: N.48, D.51 Ligands: MG.2, MG.10 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain I Metal complexes: E:D.51, A:D.51, I:D.51 MG.24: 6 residues within 4Å: Chain B: N.48, D.51 Chain C: N.48, D.51 Chain L: N.48, D.51 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain C, 1 interactions with chain B Metal complexes: L:D.51, C:D.51, B:D.51

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 8 residues within 4Å: Chain A: R.50, L.54 Chain E: R.50, L.54 Chain I: R.50, L.54 Ligands: CL.11, CL.19 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: R.50 Chain C: R.50, L.54 Chain L: R.50 Ligand excluded by PLIP CL.11: 8 residues within 4Å: Chain A: R.50, L.54 Chain E: R.50, L.54 Chain I: R.50, L.54 Ligands: CL.3, CL.19 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain D: R.50 Chain F: R.50 Chain G: R.50, L.54 Ligand excluded by PLIP CL.19: 8 residues within 4Å: Chain A: R.50, L.54 Chain E: R.50, L.54 Chain I: R.50, L.54 Ligands: CL.3, CL.11 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain H: R.50 Chain J: R.50 Chain K: R.50, L.54 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roy, S. et al., Structural studies on the second Mycobacterium smegmatis Dps: invariant and variable features of structure, assembly and function. J.Mol.Biol. (2008)

Release Date

2008-04-22

Peptides

Starvation-inducible DNA-binding protein or fine tangled pili major subunit: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Starvation-inducible DNA-binding protein or fine tangled pili major subunit

Related Entries With Identical Sequence