SMTL ID : 1tkk.1

The Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Glu Epimerase from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.160, D.191, E.219, D.244 Ligands: GLU.3 5 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: GLU.3, A:D.191, A:E.219, A:D.244, H2O.1 MG.4: 8 residues within 4Å: Chain B: K.160, K.162, D.191, N.193, E.219, D.244, N.266 Ligands: GLU.6 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.191, B:E.219, B:D.244, GLU.6, H2O.8 MG.7: 7 residues within 4Å: Chain C: K.160, D.191, N.193, E.219, D.244, K.268 Ligands: GLU.9 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:D.191, C:E.219, C:D.244, GLU.9, H2O.14 MG.10: 6 residues within 4Å: Chain D: K.160, D.191, N.193, E.219, D.244 Ligands: GLU.12 5 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: D:D.191, D:E.219, D:D.244, GLU.12, H2O.22 MG.13: 6 residues within 4Å: Chain E: K.160, D.191, N.193, E.219, D.244 Ligands: GLU.15 5 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: E:D.191, E:E.219, E:D.244, GLU.15, H2O.29 MG.16: 6 residues within 4Å: Chain F: K.160, D.191, N.193, E.219, D.244 Ligands: GLU.18 5 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: GLU.18, F:D.191, F:E.219, F:D.244, H2O.38 MG.19: 6 residues within 4Å: Chain G: K.160, D.191, E.219, D.244, K.268 Ligands: GLU.21 5 PLIP interactions: 3 interactions with chain G, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: G:D.191, G:E.219, G:D.244, GLU.21, H2O.45 MG.22: 5 residues within 4Å: Chain H: K.160, D.191, E.219, D.244 Ligands: GLU.24 5 PLIP interactions: 3 interactions with chain H, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: H:D.191, H:E.219, H:D.244, GLU.24, H2O.51

8 x ALA: ALANINE(Non-covalent)

ALA.2: 9 residues within 4Å: Chain A: F.19, T.135, K.160, K.162, S.296, I.298, D.321, D.323 Ligands: GLU.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.298 Hydrogen bonds: A:K.160, A:K.162, A:D.323 ALA.5: 9 residues within 4Å: Chain B: F.19, T.135, K.160, K.162, S.296, D.321, D.323, M.327 Ligands: GLU.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.19 Hydrogen bonds: B:K.160, B:K.162, B:D.323 Water bridges: B:A.324 ALA.8: 8 residues within 4Å: Chain C: F.19, T.135, K.160, K.162, S.296, D.321, D.323 Ligands: GLU.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.135, C:K.160, C:K.162, C:D.323 ALA.11: 8 residues within 4Å: Chain D: F.19, T.135, K.160, K.162, S.296, D.321, D.323 Ligands: GLU.12 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.19 Hydrogen bonds: D:T.135, D:K.160, D:K.162, D:D.323 Water bridges: D:A.324 ALA.14: 10 residues within 4Å: Chain E: F.19, T.135, K.160, K.162, S.296, I.298, D.321, D.323, M.327 Ligands: GLU.15 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.19, E:I.298 Hydrogen bonds: E:K.160, E:K.162, E:D.323 Water bridges: E:A.324 ALA.17: 9 residues within 4Å: Chain F: F.19, T.135, K.160, K.162, S.296, I.298, D.321, D.323 Ligands: GLU.18 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:F.19, F:I.298 Hydrogen bonds: F:T.135, F:K.160, F:K.162, F:D.323 ALA.20: 9 residues within 4Å: Chain G: F.19, T.135, K.160, K.162, S.296, I.298, D.321, D.323 Ligands: GLU.21 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:F.19, G:I.298 Hydrogen bonds: G:T.135, G:K.160, G:K.162, G:D.323 Water bridges: G:A.324 ALA.23: 8 residues within 4Å: Chain H: F.19, T.135, K.160, K.162, S.296, D.321, D.323 Ligands: GLU.24 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:T.135, H:K.160, H:K.162, H:D.323

8 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.3: 14 residues within 4Å: Chain A: F.19, R.24, I.54, K.160, K.162, D.191, E.219, D.244, K.268, S.296, M.297, I.298 Ligands: MG.1, ALA.2 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.19 Hydrogen bonds: A:K.160, A:K.162, A:K.268, A:S.296, A:I.298 Water bridges: A:D.321, A:D.321 Salt bridges: A:R.24 GLU.6: 15 residues within 4Å: Chain B: F.19, R.24, I.54, K.160, K.162, D.191, E.219, D.244, N.266, K.268, S.296, M.297, I.298 Ligands: MG.4, ALA.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.19 Hydrogen bonds: B:K.160, B:K.162, B:N.266, B:K.268, B:S.296, B:I.298 Water bridges: B:D.321, B:D.321 Salt bridges: B:R.24 GLU.9: 15 residues within 4Å: Chain C: F.19, R.24, I.54, K.160, K.162, D.191, E.219, D.244, K.268, S.296, M.297, I.298, D.321 Ligands: MG.7, ALA.8 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:F.19, C:F.19 Hydrogen bonds: C:K.160, C:K.162, C:D.191, C:N.266, C:K.268, C:S.296, C:I.298 Water bridges: C:S.296 Salt bridges: C:R.24 GLU.12: 14 residues within 4Å: Chain D: F.19, R.24, I.54, K.160, K.162, D.191, E.219, D.244, K.268, S.296, M.297, I.298 Ligands: MG.10, ALA.11 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:F.19 Hydrogen bonds: D:K.160, D:K.162, D:N.266, D:K.268, D:S.296, D:I.298 Water bridges: D:S.296 Salt bridges: D:R.24 GLU.15: 15 residues within 4Å: Chain E: F.19, R.24, I.54, K.160, K.162, D.191, E.219, D.244, N.266, K.268, S.296, M.297, I.298 Ligands: MG.13, ALA.14 9 PLIP interactions: 9 interactions with chain E, Hydrogen bonds: E:K.160, E:K.162, E:N.266, E:K.268, E:S.296, E:I.298, E:D.321 Water bridges: E:S.296 Salt bridges: E:R.24 GLU.18: 15 residues within 4Å: Chain F: F.19, R.24, I.54, K.160, K.162, D.191, E.219, D.244, K.268, S.296, M.297, I.298, D.321 Ligands: MG.16, ALA.17 9 PLIP interactions: 9 interactions with chain F, Hydrogen bonds: F:K.160, F:K.162, F:K.268, F:S.296, F:I.298, F:D.321 Water bridges: F:N.266, F:S.296 Salt bridges: F:R.24 GLU.21: 14 residues within 4Å: Chain G: F.19, R.24, I.54, K.160, K.162, D.191, E.219, D.244, K.268, S.296, M.297, I.298 Ligands: MG.19, ALA.20 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:K.160, G:K.162, G:K.268, G:S.296, G:I.298 Water bridges: G:N.266, G:S.296 Salt bridges: G:R.24 GLU.24: 14 residues within 4Å: Chain H: F.19, R.24, I.54, K.160, K.162, D.191, E.219, D.244, K.268, S.296, M.297, I.298 Ligands: MG.22, ALA.23 9 PLIP interactions: 9 interactions with chain H, Hydrophobic interactions: H:F.19 Hydrogen bonds: H:K.160, H:K.162, H:K.268, H:S.296, H:I.298 Water bridges: H:N.266, H:S.296 Salt bridges: H:R.24

Links

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Citation

Klenchin, V.A. et al., Evolution of Enzymatic Activities in the Enolase Superfamily: Structure of a Substrate-Liganded Complex of the l-Ala-d/l-Glu Epimerase from Bacillus subtilis(,). Biochemistry (2004)

Release Date

2004-08-31

Peptides

similar to chloromuconate cycloisomerase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

similar to chloromuconate cycloisomerase

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