SMTL ID : 2v15.1

Terbium binding in Streptococcus suis Dpr protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-12-mer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: H.40, H.52 Chain C: E.71 Chain H: M.154 Ligands: TB.5 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: E.71 Chain C: H.40, H.52 Ligands: TB.2 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: H.40, H.52 Chain D: E.71 Ligands: TB.7 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: E.71 Chain D: H.40, H.52 Ligands: TB.4 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain E: H.40, H.52 Chain G: E.71 Chain L: W.153, M.154 Ligands: TB.18 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain E: D.67, E.71 Ligands: TB.13 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain H: G.45, T.103, I.104 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain D: W.153, M.154 Chain I: H.40, H.52 Chain K: E.71 Ligands: TB.27 Ligand excluded by PLIP CL.24: 6 residues within 4Å: Chain A: W.153, M.154 Chain I: E.71 Chain K: H.40, H.52 Ligands: TB.23 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain B: W.153, M.154 Chain J: H.40, H.52 Chain L: E.71 Ligands: TB.30 Ligand excluded by PLIP

12 x TB: TERBIUM(III) ION(Non-covalent)

TB.2: 4 residues within 4Å: Chain A: D.67, E.71 Chain C: H.40 Ligands: CL.6 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.40, A:D.67, A:E.71, H2O.1, H2O.5 TB.4: 4 residues within 4Å: Chain B: D.67, E.71 Chain D: H.40 Ligands: CL.9 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:D.67, B:E.71, B:E.71, D:H.40, H2O.7 TB.5: 4 residues within 4Å: Chain A: H.40 Chain C: D.67, E.71 Ligands: CL.1 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.67, C:E.71, A:H.40, H2O.1, H2O.1 TB.7: 4 residues within 4Å: Chain B: H.40 Chain D: D.67, E.71 Ligands: CL.8 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.67, D:E.71, B:H.40, H2O.3, H2O.7 TB.13: 4 residues within 4Å: Chain E: D.67, E.71 Chain G: H.40 Ligands: CL.14 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: E:D.67, E:E.71, G:H.40, H2O.13, H2O.14 TB.15: 3 residues within 4Å: Chain F: D.67, E.71 Chain H: H.40 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: F:D.67, F:D.67, H:H.40, H2O.11, H2O.15 TB.18: 4 residues within 4Å: Chain E: H.40 Chain G: D.67, E.71 Ligands: CL.12 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: E:H.40, G:D.67, G:D.67, H2O.9, H2O.14 TB.19: 3 residues within 4Å: Chain F: H.40 Chain H: D.67, E.71 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: H:D.67, H:E.71, F:H.40, H2O.11, H2O.11 TB.23: 4 residues within 4Å: Chain I: D.67, E.71 Chain K: H.40 Ligands: CL.24 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: I:D.67, I:E.71, K:H.40, H2O.17, H2O.17 TB.26: 3 residues within 4Å: Chain J: D.67, E.71 Chain L: H.40 5 PLIP interactions: 2 interactions with chain J, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: J:D.67, J:E.71, L:H.40, H2O.23, H2O.23 TB.27: 4 residues within 4Å: Chain I: H.40 Chain K: D.67, E.71 Ligands: CL.22 5 PLIP interactions: 2 interactions with chain K, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: K:D.67, K:E.71, I:H.40, H2O.17, H2O.21 TB.30: 4 residues within 4Å: Chain J: H.40 Chain L: D.67, E.71 Ligands: CL.25 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: L:D.67, L:E.71, J:H.40, H2O.19, H2O.19

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 1 residues within 4Å: Chain B: E.106 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.106, B:E.106 CA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.20: 1 residues within 4Å: Chain H: N.101 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:N.101 CA.29: 2 residues within 4Å: Chain K: D.17, E.132 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.17, K:E.132

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

EPE.10: 6 residues within 4Å: Chain D: R.46, G.47 Chain G: G.47 Chain I: R.46, G.47, I.50 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain D Water bridges: I:R.46, D:R.46 Hydrogen bonds: D:R.46 EPE.11: 7 residues within 4Å: Chain C: R.46, G.47, I.50 Chain E: R.46, G.47 Chain L: G.47, I.50 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.46, C:R.46 EPE.16: 7 residues within 4Å: Chain B: R.46, I.50 Chain F: R.46, G.47, I.50 Chain J: R.46, G.47 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:G.47 Water bridges: B:R.46, F:G.47, F:G.47 EPE.28: 7 residues within 4Å: Chain A: R.46, G.47, I.50 Chain H: G.47 Chain K: R.46, G.47, E.105 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain K Water bridges: H:R.46, H:G.47 Hydrogen bonds: K:E.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Havukainen, H. et al., Structural basis of the zinc- and terbium-mediated inhibition of ferroxidase activity in Dps ferritin-like proteins. Protein Sci. (2008)

Release Date

2008-06-10

Peptides

DNA PROTECTION DURING STARVATION PROTEIN: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

DNA PROTECTION DURING STARVATION PROTEIN

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