SMTL ID : 2xkq.1

Crystal structure of Streptococcus suis Dpr with manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-12-mer

Ligands

12 x MN3: MANGANESE (III) ION(Non-covalent)

MN3.1: 3 residues within 4Å: Chain A: D.67, E.71 Chain C: H.40 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:D.67, A:D.67, A:E.71, C:H.40 MN3.4: 3 residues within 4Å: Chain B: D.67, E.71 Chain D: H.40 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:D.67, B:D.67, B:E.71, D:H.40, H2O.4 MN3.7: 3 residues within 4Å: Chain A: H.40 Chain C: D.67, E.71 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:D.67, C:D.67, C:E.71, A:H.40 MN3.10: 3 residues within 4Å: Chain B: H.40 Chain D: D.67, E.71 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Metal complexes: D:D.67, D:D.67, D:E.71, B:H.40 MN3.14: 3 residues within 4Å: Chain E: D.67, E.71 Chain G: H.40 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain G Metal complexes: E:D.67, E:D.67, E:E.71, G:H.40 MN3.15: 3 residues within 4Å: Chain F: D.67, E.71 Chain H: H.40 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain H Metal complexes: F:D.67, F:E.71, H:H.40 MN3.18: 3 residues within 4Å: Chain E: H.40 Chain G: D.67, E.71 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E Metal complexes: G:D.67, G:E.71, E:H.40 MN3.20: 3 residues within 4Å: Chain F: H.40 Chain H: D.67, E.71 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain H Metal complexes: F:H.40, H:D.67, H:E.71 MN3.21: 3 residues within 4Å: Chain I: D.67, E.71 Chain K: H.40 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain K Metal complexes: I:D.67, I:D.67, I:E.71, K:H.40 MN3.23: 3 residues within 4Å: Chain J: D.67, E.71 Chain L: H.40 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain L Metal complexes: J:D.67, J:D.67, J:E.71, L:H.40 MN3.25: 3 residues within 4Å: Chain I: H.40 Chain K: D.67, E.71 5 PLIP interactions: 1 interactions with chain I, 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: I:H.40, K:D.67, K:D.67, K:E.71, H2O.14 MN3.26: 3 residues within 4Å: Chain J: H.40 Chain L: D.67, E.71 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain L Metal complexes: J:H.40, L:D.67, L:E.71

4 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.8: 1 residues within 4Å: Chain C: L.159 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain D: T.103, I.104 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain I: Q.161, A.162, K.164 Ligand excluded by PLIP

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

EPE.3: 5 residues within 4Å: Chain B: R.46, G.47 Chain F: R.46, G.47 Chain J: G.47 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain F Water bridges: J:R.46, J:G.47, J:E.158, F:R.46 EPE.9: 6 residues within 4Å: Chain D: G.47, I.50 Chain G: R.46, G.47 Chain I: G.47, I.50 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.46 EPE.13: 8 residues within 4Å: Chain C: R.46, G.47 Chain E: R.46, G.47, I.50 Chain L: R.46, G.47, I.50 1 PLIP interactions: 1 interactions with chain E Water bridges: E:R.46 EPE.24: 7 residues within 4Å: Chain A: R.46, G.47 Chain H: R.46, G.47 Chain K: R.46, G.47, I.50 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain K, 1 interactions with chain A Water bridges: H:G.47, H:G.47, H:E.158, K:R.46, A:R.46

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

CA.5: 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.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 2 residues within 4Å: Chain D: D.17, E.132 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.17, D:E.132 CA.16: 1 residues within 4Å: Chain F: L.159 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:L.159, H2O.10, H2O.11, H2O.11 CA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.19: 1 residues within 4Å: Chain G: N.101 No protein-ligand interaction detected (PLIP)

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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