SMTL ID : 5hjh.1

Dps4 from Nostoc punctiforme in complex with Fe ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-12-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: H.74, E.78 Chain B: H.47, H.59 Ligands: FE.5 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.47, A:H.74, A:E.78, H2O.4, H2O.7 FE.3: 5 residues within 4Å: Chain A: H.47, H.59 Chain B: H.74, E.78 Ligands: FE.4 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.47, B:H.74, B:E.78, H2O.2, H2O.8 FE.4: 4 residues within 4Å: Chain A: H.59 Chain B: E.78 Chain K: H.160 Ligands: FE.3 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: A:H.59, B:E.78, K:H.160, H2O.1, H2O.2 FE.5: 4 residues within 4Å: Chain A: E.78 Chain B: H.59 Chain F: H.160 Ligands: FE.1 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: F:H.160, A:E.78, B:H.59, H2O.2, H2O.7 FE.6: 5 residues within 4Å: Chain C: H.74, E.78 Chain D: H.47, H.59 Ligands: FE.8 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:H.74, C:E.78, D:H.47, H2O.15 FE.7: 4 residues within 4Å: Chain C: H.59 Chain D: E.78 Chain H: H.160 Ligands: FE.9 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: H:H.160, D:E.78, C:H.59, H2O.11, H2O.29 FE.8: 4 residues within 4Å: Chain A: H.160 Chain C: E.78 Chain D: H.59 Ligands: FE.6 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:E.78, D:H.59, H2O.9, H2O.15, H2O.15 FE.9: 5 residues within 4Å: Chain C: H.47, H.59 Chain D: H.74, E.78 Ligands: FE.7 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:H.74, D:E.78, C:H.47, H2O.11, H2O.14 FE.10: 5 residues within 4Å: Chain E: H.74, E.78 Chain F: H.47, H.59 Ligands: FE.14 5 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: F:H.47, E:H.74, E:E.78, H2O.18, H2O.22 FE.12: 5 residues within 4Å: Chain E: H.47, H.59 Chain F: H.74, E.78 Ligands: FE.13 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: F:H.74, F:E.78, E:H.47, H2O.17, H2O.22 FE.13: 4 residues within 4Å: Chain C: H.160 Chain E: H.59 Chain F: E.78 Ligands: FE.12 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: C:H.160, F:E.78, E:H.59, H2O.16, H2O.17 FE.14: 4 residues within 4Å: Chain E: E.78 Chain F: H.59 Chain J: H.160 Ligands: FE.10 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: F:H.59, E:E.78, J:H.160, H2O.17, H2O.22 FE.15: 5 residues within 4Å: Chain G: H.74, E.78 Chain H: H.47, H.59 Ligands: FE.17 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:H.74, G:E.78, H:H.47, H2O.29 FE.16: 4 residues within 4Å: Chain G: H.59 Chain H: E.78 Chain L: H.160 Ligands: FE.18 5 PLIP interactions: 1 interactions with chain L, 1 interactions with chain H, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: L:H.160, H:E.78, G:H.59, H2O.26, H2O.43 FE.17: 4 residues within 4Å: Chain E: H.160 Chain G: E.78 Chain H: H.59 Ligands: FE.15 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: G:E.78, H:H.59, H2O.24, H2O.29, H2O.29 FE.18: 5 residues within 4Å: Chain G: H.47, H.59 Chain H: H.74, E.78 Ligands: FE.16 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: G:H.47, H:H.74, H:E.78, H2O.26, H2O.29 FE.19: 5 residues within 4Å: Chain I: H.74, E.78 Chain J: H.47, H.59 Ligands: FE.23 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: I:H.74, I:E.78, J:H.47, H2O.33, H2O.36 FE.21: 5 residues within 4Å: Chain I: H.47, H.59 Chain J: H.74, E.78 Ligands: FE.22 5 PLIP interactions: 1 interactions with chain I, 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: I:H.47, J:H.74, J:E.78, H2O.31, H2O.37 FE.22: 4 residues within 4Å: Chain G: H.160 Chain I: H.59 Chain J: E.78 Ligands: FE.21 5 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: I:H.59, J:E.78, G:H.160, H2O.30, H2O.31 FE.23: 4 residues within 4Å: Chain B: H.160 Chain I: E.78 Chain J: H.59 Ligands: FE.19 5 PLIP interactions: 1 interactions with chain I, 1 interactions with chain B, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: I:E.78, B:H.160, J:H.59, H2O.31, H2O.36 FE.24: 5 residues within 4Å: Chain K: H.74, E.78 Chain L: H.47, H.59 Ligands: FE.26 4 PLIP interactions: 2 interactions with chain K, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: K:H.74, K:E.78, L:H.47, H2O.44 FE.25: 4 residues within 4Å: Chain D: H.160 Chain K: H.59 Chain L: E.78 Ligands: FE.27 5 PLIP interactions: 1 interactions with chain L, 1 interactions with chain D, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: L:E.78, D:H.160, K:H.59, H2O.14, H2O.40 FE.26: 4 residues within 4Å: Chain I: H.160 Chain K: E.78 Chain L: H.59 Ligands: FE.24 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L, 3 Ligand-Water interactions Metal complexes: K:E.78, L:H.59, H2O.38, H2O.44, H2O.44 FE.27: 5 residues within 4Å: Chain K: H.47, H.59 Chain L: H.74, E.78 Ligands: FE.25 5 PLIP interactions: 1 interactions with chain K, 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: K:H.47, L:H.74, L:E.78, H2O.40, H2O.43

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 7 residues within 4Å: Chain A: Y.11, D.12, N.13, L.16, L.17, D.18, R.19 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.12, A:N.13, A:N.13 Water bridges: A:N.13, A:L.16 Salt bridges: A:R.19 EPE.11: 7 residues within 4Å: Chain E: Y.11, D.12, N.13, L.16, L.17, D.18, R.19 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:D.12, E:N.13, E:N.13 Water bridges: E:N.13, E:L.16 Salt bridges: E:R.19 EPE.20: 7 residues within 4Å: Chain I: Y.11, D.12, N.13, L.16, L.17, D.18, R.19 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:D.12, I:N.13, I:N.13 Water bridges: I:N.13, I:L.16 Salt bridges: I:R.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Howe, C. et al., Dps4 from Nostoc punctiforme in complex with Fe ions. To Be Published

Release Date

2017-01-25

Peptides

Ferritin, Dps family protein: 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

Ferritin, Dps family protein