SMTL ID : 1moj.1

Crystal structure of an archaeal dps-homologue from Halobacterium salinarum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-12-mer

Ligands

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

FE.1: 3 residues within 4Å: Chain A: D.79, E.83 Chain B: H.52 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.79, A:E.83, B:H.52, H2O.2, H2O.5 FE.2: 3 residues within 4Å: Chain A: E.154 Chain C: E.154 Chain H: E.154 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: H:E.154, A:E.154, C:E.154, H2O.8, H2O.22 FE.4: 3 residues within 4Å: Chain A: H.52 Chain B: D.79, E.83 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.79, B:E.83, A:H.52, H2O.5, H2O.5 FE.5: 5 residues within 4Å: Chain B: E.154 Chain F: E.154 Chain J: E.154 Ligands: FE.17, FE.29 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain J, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: B:E.154, J:E.154, F:E.154, H2O.16, H2O.28 FE.7: 3 residues within 4Å: Chain C: D.79, E.83 Chain D: H.52 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:D.79, C:E.83, D:H.52, H2O.8, H2O.8 FE.11: 3 residues within 4Å: Chain C: H.52 Chain D: D.79, E.83 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.79, D:E.83, C:H.52, H2O.10, H2O.11 FE.13: 3 residues within 4Å: Chain E: D.79, E.83 Chain F: H.52 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: E:D.79, E:E.83, F:H.52, H2O.14, H2O.16 FE.14: 3 residues within 4Å: Chain E: E.154 Chain G: E.154 Chain L: E.154 5 PLIP interactions: 1 interactions with chain L, 1 interactions with chain E, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: L:E.154, E:E.154, G:E.154, H2O.19, H2O.34 FE.16: 3 residues within 4Å: Chain E: H.52 Chain F: D.79, E.83 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: F:D.79, F:E.83, E:H.52, H2O.16, H2O.16 FE.17: 5 residues within 4Å: Chain B: E.154 Chain F: E.154 Chain J: E.154 Ligands: FE.5, FE.29 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain B, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: J:E.154, B:E.154, F:E.154, H2O.5, H2O.28 FE.19: 3 residues within 4Å: Chain G: D.79, E.83 Chain H: H.52 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: G:D.79, G:E.83, H:H.52, H2O.19, H2O.19 FE.23: 3 residues within 4Å: Chain G: H.52 Chain H: D.79, E.83 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: H:D.79, H:E.83, G:H.52, H2O.22, H2O.22 FE.25: 3 residues within 4Å: Chain I: D.79, E.83 Chain J: H.52 5 PLIP interactions: 1 interactions with chain J, 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: J:H.52, I:D.79, I:E.83, H2O.25, H2O.28 FE.26: 3 residues within 4Å: Chain D: E.154 Chain I: E.154 Chain K: E.154 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain D, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: K:E.154, D:E.154, I:E.154, H2O.11, H2O.31 FE.28: 3 residues within 4Å: Chain I: H.52 Chain J: D.79, E.83 5 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: J:D.79, J:E.83, I:H.52, H2O.27, H2O.27 FE.29: 5 residues within 4Å: Chain B: E.154 Chain F: E.154 Chain J: E.154 Ligands: FE.5, FE.17 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain B, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: J:E.154, B:E.154, F:E.154, H2O.5, H2O.16 FE.31: 3 residues within 4Å: Chain K: D.79, E.83 Chain L: H.52 5 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: L:H.52, K:D.79, K:E.83, H2O.30, H2O.30 FE.35: 3 residues within 4Å: Chain K: H.52 Chain L: D.79, E.83 5 PLIP interactions: 1 interactions with chain K, 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: K:H.52, L:D.79, L:E.83, H2O.33, H2O.33

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

NA.3: 5 residues within 4Å: Chain A: E.59 Chain D: E.59, V.176 Chain J: E.59, V.176 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain J Hydrogen bonds: A:E.59, J:E.59, J:E.59 NA.10: 8 residues within 4Å: Chain C: E.59, V.176 Chain G: E.59, V.176 Chain K: E.59, V.176 Ligands: NA.22, NA.34 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain G, 2 interactions with chain C Hydrogen bonds: K:E.59, G:E.59, C:E.59, C:E.59 NA.15: 5 residues within 4Å: Chain B: E.59, V.176 Chain E: E.59 Chain H: E.59, V.176 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:E.59, B:E.59, B:E.59 NA.22: 8 residues within 4Å: Chain C: E.59, V.176 Chain G: E.59, V.176 Chain K: E.59, V.176 Ligands: NA.10, NA.34 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain C, 1 interactions with chain K Hydrogen bonds: G:E.59, G:E.59, C:E.59, K:E.59 NA.27: 5 residues within 4Å: Chain F: E.59, V.176 Chain I: E.59 Chain L: E.59, V.176 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain F Hydrogen bonds: I:E.59, I:E.59, F:E.59 NA.34: 8 residues within 4Å: Chain C: E.59, V.176 Chain G: E.59, V.176 Chain K: E.59, V.176 Ligands: NA.10, NA.22 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain G, 1 interactions with chain K Hydrogen bonds: C:E.59, G:E.59, G:E.59, K:E.59

12 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain B: H.168 Chain E: E.56 Chain F: Q.86 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: E:E.56, B:H.168, H2O.6, H2O.6, H2O.6 MG.8: 3 residues within 4Å: Chain A: H.168 Chain C: Q.86 Chain D: E.56 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: D:E.56, A:H.168, H2O.3, H2O.3, H2O.9 MG.9: 3 residues within 4Å: Chain C: H.168 Chain G: E.56 Chain H: Q.86 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: C:H.168, G:E.56, H2O.7, H2O.9, H2O.9 MG.12: 3 residues within 4Å: Chain D: H.168 Chain I: Q.86 Chain J: E.56 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain J, 3 Ligand-Water interactions Metal complexes: D:H.168, J:E.56, H2O.11, H2O.11, H2O.12 MG.18: 3 residues within 4Å: Chain F: H.168 Chain I: E.56 Chain J: Q.86 5 PLIP interactions: 1 interactions with chain I, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: I:E.56, F:H.168, H2O.17, H2O.17, H2O.17 MG.20: 3 residues within 4Å: Chain E: H.168 Chain G: Q.86 Chain H: E.56 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: E:H.168, H:E.56, H2O.14, H2O.14, H2O.20 MG.21: 3 residues within 4Å: Chain G: H.168 Chain K: E.56 Chain L: Q.86 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: G:H.168, K:E.56, H2O.19, H2O.20, H2O.20 MG.24: 3 residues within 4Å: Chain A: Q.86 Chain B: E.56 Chain H: H.168 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: H:H.168, B:E.56, H2O.22, H2O.23, H2O.23 MG.30: 3 residues within 4Å: Chain A: E.56 Chain B: Q.86 Chain J: H.168 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: J:H.168, A:E.56, H2O.29, H2O.29, H2O.29 MG.32: 3 residues within 4Å: Chain I: H.168 Chain K: Q.86 Chain L: E.56 5 PLIP interactions: 1 interactions with chain I, 1 interactions with chain L, 3 Ligand-Water interactions Metal complexes: I:H.168, L:E.56, H2O.26, H2O.26, H2O.32 MG.33: 3 residues within 4Å: Chain C: E.56 Chain D: Q.86 Chain K: H.168 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: K:H.168, C:E.56, H2O.30, H2O.31, H2O.32 MG.36: 3 residues within 4Å: Chain E: Q.86 Chain F: E.56 Chain L: H.168 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain L, 3 Ligand-Water interactions Metal complexes: F:E.56, L:H.168, H2O.34, H2O.34, H2O.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeth, K. et al., Iron-oxo clusters biomineralizing on protein surfaces: Structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states. Proc.Natl.Acad.Sci.USA (2004)

Release Date

2004-04-20

Peptides

Dps-like ferritin: 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

Dps-like ferritin

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