SMTL ID : 2xjm.1

Crystal structure of Streptococcus suis Dpr with cobalt

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-12-mer

Ligands

12 x CO: COBALT (II) ION(Non-covalent)

CO.1: 3 residues within 4Å: Chain A: D.67, E.71 Chain C: H.40 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:D.67, A:D.67, A:E.71, C:H.40, H2O.3 CO.3: 3 residues within 4Å: Chain B: D.67, E.71 Chain D: H.40 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.67, B:E.71, D:H.40, H2O.6, H2O.9 CO.5: 3 residues within 4Å: Chain A: H.40 Chain C: D.67, E.71 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:D.67, C:D.67, C:E.71, A:H.40, H2O.1 CO.7: 4 residues within 4Å: Chain B: H.40, H.52 Chain D: D.67, E.71 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.12, H2O.12 CO.9: 3 residues within 4Å: Chain E: D.67, E.71 Chain G: H.40 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: E:D.67, E:D.67, E:E.71, G:H.40, H2O.13 CO.11: 4 residues within 4Å: Chain F: D.67, E.71 Chain H: H.40, D.56 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain H Metal complexes: F:D.67, F:D.67, F:E.71, H:H.40 CO.14: 3 residues within 4Å: Chain E: H.40 Chain G: D.67, E.71 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:D.67, G:E.71, E:H.40, H2O.17, H2O.18 CO.15: 3 residues within 4Å: Chain F: H.40 Chain H: D.67, E.71 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: H:D.67, H:D.67, H:E.71, F:H.40, H2O.14 CO.18: 3 residues within 4Å: Chain I: D.67, E.71 Chain K: H.40 5 PLIP interactions: 1 interactions with chain K, 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: K:H.40, I:D.67, I:D.67, I:E.71, H2O.21 CO.22: 3 residues within 4Å: Chain J: D.67, E.71 Chain L: H.40 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: J:D.67, J:D.67, J:E.71, L:H.40, H2O.24 CO.26: 4 residues within 4Å: Chain I: H.40, D.56 Chain K: D.67, E.71 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain I Metal complexes: K:D.67, K:D.67, K:E.71, I:H.40 CO.27: 4 residues within 4Å: Chain J: H.40, H.52 Chain L: D.67, E.71 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.30, H2O.31

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

CL.2: 4 residues within 4Å: Chain A: A.162, P.163, K.164 Chain I: G.77 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain I: Q.161, A.162, K.164 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain J: R.44, G.45, T.103, I.104, E.105 Ligand excluded by PLIP

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

CA.4: 1 residues within 4Å: Chain B: E.106 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.106, B:E.106, H2O.5 CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.10: 2 residues within 4Å: Chain E: A.16, E.132 No protein-ligand interaction detected (PLIP) CA.12: 1 residues within 4Å: Chain F: L.159 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:L.159, H2O.16, H2O.16 CA.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.16: 1 residues within 4Å: Chain H: N.101 No protein-ligand interaction detected (PLIP) CA.20: 1 residues within 4Å: Chain I: N.101 No protein-ligand interaction detected (PLIP) CA.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EPE.8: 9 residues within 4Å: Chain C: R.46, G.47, I.50 Chain E: R.46, G.47, I.50 Chain L: R.46, G.47, I.50 No protein-ligand interaction detected (PLIP) EPE.17: 7 residues within 4Å: Chain D: R.46, G.47 Chain G: R.46, G.47, I.50 Chain I: R.46, G.47 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain I, 2 interactions with chain D Water bridges: G:G.47, I:E.158, D:G.47, D:G.47 EPE.21: 5 residues within 4Å: Chain B: G.47 Chain F: R.46, G.47 Chain J: R.46, G.47 5 PLIP interactions: 2 interactions with chain J, 2 interactions with chain F, 1 interactions with chain B Water bridges: J:G.47, J:G.47, F:R.46, F:G.47, B:R.46 EPE.25: 7 residues within 4Å: Chain A: R.46, G.47 Chain H: R.46, G.47 Chain K: R.46, G.47, I.50 2 PLIP interactions: 2 interactions with chain K Water bridges: K:R.46, K:G.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haikarainen, T. et al., Structural and Thermodynamic Characterization of Metal Ion Binding in Streptococcus Suis Dpr. J.Mol.Biol. (2011)

Release Date

2010-11-24

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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