SMTL ID : 1vei.1

Mycobacterium smegmatis Dps

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-12-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: D.66, E.70 Chain J: K.36, H.39, D.55 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain J Metal complexes: A:D.66, A:D.66, A:E.70, J:H.39 FE.2: 3 residues within 4Å: Chain A: D.66 Chain J: K.36, R.62 No protein-ligand interaction detected (PLIP) FE.4: 5 residues within 4Å: Chain B: D.66, E.70 Chain E: K.36, H.39, D.55 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain B Metal complexes: E:H.39, B:D.66, B:D.66, B:E.70 FE.5: 3 residues within 4Å: Chain B: D.66 Chain E: K.36, R.62 No protein-ligand interaction detected (PLIP) FE.7: 5 residues within 4Å: Chain C: D.66, E.70 Chain I: K.36, H.39, D.55 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain I Metal complexes: C:D.66, C:D.66, C:E.70, I:H.39 FE.8: 3 residues within 4Å: Chain C: D.66 Chain I: K.36, R.62 No protein-ligand interaction detected (PLIP) FE.10: 5 residues within 4Å: Chain D: D.66, E.70 Chain G: K.36, H.39, D.55 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain G Metal complexes: D:D.66, D:D.66, D:E.70, G:H.39 FE.11: 3 residues within 4Å: Chain D: D.66 Chain G: K.36, R.62 No protein-ligand interaction detected (PLIP) FE.13: 5 residues within 4Å: Chain B: K.36, H.39, D.55 Chain E: D.66, E.70 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Metal complexes: E:D.66, E:D.66, E:E.70, B:H.39 FE.14: 3 residues within 4Å: Chain B: K.36, R.62 Chain E: D.66 No protein-ligand interaction detected (PLIP) FE.16: 5 residues within 4Å: Chain F: D.66, E.70 Chain L: K.36, H.39, D.55 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain L Metal complexes: F:D.66, F:D.66, F:E.70, L:H.39 FE.17: 3 residues within 4Å: Chain F: D.66 Chain L: K.36, R.62 No protein-ligand interaction detected (PLIP) FE.19: 5 residues within 4Å: Chain D: K.36, H.39, D.55 Chain G: D.66, E.70 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain G Metal complexes: D:H.39, G:D.66, G:D.66, G:E.70 FE.20: 3 residues within 4Å: Chain D: K.36, R.62 Chain G: D.66 No protein-ligand interaction detected (PLIP) FE.22: 5 residues within 4Å: Chain H: D.66, E.70 Chain K: K.36, H.39, D.55 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain K Metal complexes: H:D.66, H:D.66, H:E.70, K:H.39 FE.23: 3 residues within 4Å: Chain H: D.66 Chain K: K.36, R.62 No protein-ligand interaction detected (PLIP) FE.25: 5 residues within 4Å: Chain C: K.36, H.39, D.55 Chain I: D.66, E.70 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain C Metal complexes: I:D.66, I:D.66, I:E.70, C:H.39 FE.26: 3 residues within 4Å: Chain C: K.36, R.62 Chain I: D.66 No protein-ligand interaction detected (PLIP) FE.28: 5 residues within 4Å: Chain A: K.36, H.39, D.55 Chain J: D.66, E.70 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain A Metal complexes: J:D.66, J:D.66, J:E.70, A:H.39 FE.29: 3 residues within 4Å: Chain A: K.36, R.62 Chain J: D.66 No protein-ligand interaction detected (PLIP) FE.31: 5 residues within 4Å: Chain H: K.36, H.39, D.55 Chain K: D.66, E.70 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain K Metal complexes: H:H.39, K:D.66, K:D.66, K:E.70 FE.32: 3 residues within 4Å: Chain H: K.36, R.62 Chain K: D.66 No protein-ligand interaction detected (PLIP) FE.34: 5 residues within 4Å: Chain F: K.36, H.39, D.55 Chain L: D.66, E.70 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain F Metal complexes: L:D.66, L:D.66, L:E.70, F:H.39 FE.35: 3 residues within 4Å: Chain F: K.36, R.62 Chain L: D.66 No protein-ligand interaction detected (PLIP)

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

SO4.3: 4 residues within 4Å: Chain A: R.99 Chain J: K.77, S.78, K.80 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain A Hydrogen bonds: J:S.78 Salt bridges: J:K.77, J:K.80, A:R.99 SO4.6: 4 residues within 4Å: Chain B: R.99 Chain E: K.77, S.78, K.80 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:S.78 Salt bridges: E:K.77, E:K.80, B:R.99 SO4.9: 4 residues within 4Å: Chain C: R.99 Chain I: K.77, S.78, K.80 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain C Hydrogen bonds: I:S.78 Salt bridges: I:K.77, I:K.80, C:R.99 SO4.12: 4 residues within 4Å: Chain D: R.99 Chain G: K.77, S.78, K.80 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain D Hydrogen bonds: G:S.78 Salt bridges: G:K.77, G:K.80, D:R.99 SO4.15: 4 residues within 4Å: Chain B: K.77, S.78, K.80 Chain E: R.99 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:S.78 Salt bridges: B:K.77, B:K.80, E:R.99 SO4.18: 4 residues within 4Å: Chain F: R.99 Chain L: K.77, S.78, K.80 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain F Hydrogen bonds: L:S.78 Salt bridges: L:K.77, L:K.80, F:R.99 SO4.21: 4 residues within 4Å: Chain D: K.77, S.78, K.80 Chain G: R.99 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:S.78 Salt bridges: D:K.77, D:K.80, G:R.99 SO4.24: 4 residues within 4Å: Chain H: R.99 Chain K: K.77, S.78, K.80 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain K Salt bridges: H:R.99, K:K.77, K:K.80 Hydrogen bonds: K:S.78 SO4.27: 4 residues within 4Å: Chain C: K.77, S.78, K.80 Chain I: R.99 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain I Hydrogen bonds: C:S.78 Salt bridges: C:K.77, C:K.80, I:R.99 SO4.30: 4 residues within 4Å: Chain A: K.77, S.78, K.80 Chain J: R.99 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain J Hydrogen bonds: A:S.78 Salt bridges: A:K.77, A:K.80, J:R.99 SO4.33: 4 residues within 4Å: Chain H: K.77, S.78, K.80 Chain K: R.99 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain H Salt bridges: K:R.99, H:K.77, H:K.80 Hydrogen bonds: H:S.78 SO4.36: 4 residues within 4Å: Chain F: K.77, S.78, K.80 Chain L: R.99 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain L Hydrogen bonds: F:S.78 Salt bridges: F:K.77, F:K.80, L:R.99

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
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

starvation-induced DNA protecting protein

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