SMTL ID : 2gsh.1

Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.227, E.253, E.281 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.227, A:E.253, A:E.281, H2O.1, H2O.3 MG.4: 3 residues within 4Å: Chain B: D.227, E.253, E.281 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.227, B:E.253, B:E.281, H2O.5, H2O.7 MG.5: 3 residues within 4Å: Chain C: D.227, E.253, E.281 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.227, C:E.253, C:E.281, H2O.8, H2O.11 MG.8: 3 residues within 4Å: Chain D: D.227, E.253, E.281 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.227, D:E.253, D:E.281, H2O.13, H2O.15 MG.9: 3 residues within 4Å: Chain E: D.227, E.253, E.281 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.227, E:E.253, E:E.281, H2O.16, H2O.19 MG.12: 3 residues within 4Å: Chain F: D.227, E.253, E.281 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.227, F:E.253, F:E.281, H2O.20, H2O.23 MG.13: 3 residues within 4Å: Chain G: D.227, E.253, E.281 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.227, G:E.253, G:E.281, H2O.24, H2O.27 MG.16: 3 residues within 4Å: Chain H: D.227, E.253, E.281 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.227, H:E.253, H:E.281, H2O.28, H2O.31

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: D.233, V.234, N.235 Chain H: D.298, I.299, G.324, Q.325, L.326 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain A Hydrogen bonds: H:D.298, H:L.326, A:D.233, A:V.234, A:N.235 GOL.3: 7 residues within 4Å: Chain A: D.298, G.324, Q.325, L.326 Chain F: D.233, V.234, N.235 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:D.233, F:V.234, F:N.235, A:L.326 GOL.6: 8 residues within 4Å: Chain C: D.233, V.234, N.235 Chain F: D.298, I.299, G.324, Q.325, L.326 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:D.233, C:V.234, C:N.235, F:D.298, F:L.326 GOL.7: 7 residues within 4Å: Chain C: D.298, G.324, Q.325, L.326 Chain H: D.233, V.234, N.235 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain C Hydrogen bonds: H:D.233, H:V.234, H:N.235, C:L.326 GOL.10: 8 residues within 4Å: Chain D: D.298, I.299, G.324, Q.325, L.326 Chain E: D.233, V.234, N.235 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:D.298, D:L.326, E:D.233, E:V.234, E:N.235 GOL.11: 7 residues within 4Å: Chain B: D.233, V.234, N.235 Chain E: D.298, G.324, Q.325, L.326 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:D.298, E:L.326, B:D.233, B:V.234, B:N.235 GOL.14: 8 residues within 4Å: Chain B: D.298, I.299, G.324, Q.325, L.326 Chain G: D.233, V.234, N.235 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain B Hydrogen bonds: G:D.233, G:V.234, G:N.235, B:D.298, B:L.326 GOL.15: 7 residues within 4Å: Chain D: D.233, V.234, N.235 Chain G: D.298, G.324, Q.325, L.326 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:D.233, D:V.234, D:N.235, G:D.298, G:L.326

Links

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Citation

Patskovsky, Y. et al., Crystal Structure of L-rhamnonate dehydratase from Salmonella Typhimurium Lt2. To be Published

Release Date

2006-05-09

Peptides

L-RHAMNONATE DEHYDRATASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

L-RHAMNONATE DEHYDRATASE