SMTL ID : 3cb3.3 (2 other biounits)

Crystal structure of L-Talarate dehydratase from Polaromonas sp. JS666 complexed with Mg and L-glucarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.213, E.239, E.265 Ligands: LGT.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:E.239, A:E.265, H2O.1 MG.2: 2 residues within 4Å: Chain A: A.254, F.257 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:A.254, A:F.257, H2O.1, H2O.2, H2O.3, H2O.4 MG.4: 4 residues within 4Å: Chain B: D.213, E.239, E.265 Ligands: LGT.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:E.239, B:E.265, H2O.6 MG.5: 2 residues within 4Å: Chain B: A.254, F.257 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.254, B:F.257, H2O.6, H2O.10, H2O.10, H2O.11 MG.7: 6 residues within 4Å: Chain C: D.213, N.215, E.239, E.240, E.265 Ligands: LGT.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.213, C:E.239, C:E.265, H2O.11 MG.8: 2 residues within 4Å: Chain C: A.254, F.257 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:A.254, C:F.257, H2O.11, H2O.11, H2O.11, H2O.15 MG.10: 5 residues within 4Å: Chain D: K.182, D.213, E.239, E.265 Ligands: LGT.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.213, D:E.239, D:E.265, H2O.15 MG.11: 2 residues within 4Å: Chain D: A.254, F.257 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:A.254, D:F.257, H2O.15, H2O.15, H2O.15, H2O.15 MG.13: 4 residues within 4Å: Chain E: D.213, E.239, E.265 Ligands: LGT.15 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.213, E:E.239, E:E.265, H2O.20 MG.14: 2 residues within 4Å: Chain E: A.254, F.257 6 PLIP interactions: 2 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:A.254, E:F.257, H2O.20, H2O.21, H2O.22, H2O.23 MG.16: 4 residues within 4Å: Chain F: D.213, E.239, E.265 Ligands: LGT.18 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.213, F:E.239, F:E.265, H2O.25 MG.17: 2 residues within 4Å: Chain F: A.254, F.257 6 PLIP interactions: 2 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:A.254, F:F.257, H2O.25, H2O.29, H2O.29, H2O.30 MG.19: 6 residues within 4Å: Chain G: D.213, N.215, E.239, E.240, E.265 Ligands: LGT.21 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.213, G:E.239, G:E.265, H2O.30 MG.20: 2 residues within 4Å: Chain G: A.254, F.257 6 PLIP interactions: 2 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:A.254, G:F.257, H2O.30, H2O.31, H2O.31, H2O.34 MG.22: 5 residues within 4Å: Chain H: K.182, D.213, E.239, E.265 Ligands: LGT.24 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.213, H:E.239, H:E.265, H2O.34 MG.23: 2 residues within 4Å: Chain H: A.254, F.257 6 PLIP interactions: 2 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:A.254, H:F.257, H2O.34, H2O.35, H2O.35, H2O.35

8 x LGT: L-GLUCARIC ACID(Non-covalent)

LGT.3: 13 residues within 4Å: Chain A: I.31, K.69, K.182, K.184, D.213, N.215, E.239, E.265, H.315, E.335, F.337, W.339 Ligands: MG.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.69, A:K.69, A:D.213, A:D.213, A:E.265, A:H.315 Water bridges: A:Y.152, A:K.182, A:N.215, A:E.240, A:R.291 Salt bridges: A:K.182, A:K.184, A:H.315 LGT.6: 13 residues within 4Å: Chain B: M.44, K.69, K.182, K.184, D.213, N.215, E.239, E.265, H.315, E.335, F.337, W.339 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.69, B:K.69, B:K.184, B:K.184, B:E.265, B:H.315 Water bridges: B:E.240 Salt bridges: B:K.182, B:K.184, B:K.184, B:H.315 LGT.9: 13 residues within 4Å: Chain C: M.44, K.69, F.158, K.182, K.184, D.213, N.215, E.239, E.265, H.315, E.335, F.337 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.69, C:K.69, C:K.184, C:E.239, C:E.265, C:H.315 Water bridges: C:E.240 Salt bridges: C:K.182, C:K.184, C:K.184, C:H.315 LGT.12: 12 residues within 4Å: Chain D: K.69, K.182, K.184, D.213, N.215, E.239, E.265, H.315, E.335, F.337, W.339 Ligands: MG.10 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:K.69, D:D.213, D:E.265, D:H.315 Salt bridges: D:K.69, D:K.182, D:K.184, D:H.315 LGT.15: 13 residues within 4Å: Chain E: I.31, K.69, K.182, K.184, D.213, N.215, E.239, E.265, H.315, E.335, F.337, W.339 Ligands: MG.13 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:K.69, E:K.69, E:D.213, E:E.265, E:H.315 Water bridges: E:K.182, E:N.215, E:R.291, E:E.335 Salt bridges: E:K.182, E:K.184, E:H.315 LGT.18: 13 residues within 4Å: Chain F: M.44, K.69, K.182, K.184, D.213, N.215, E.239, E.265, H.315, E.335, F.337, W.339 Ligands: MG.16 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:K.69, F:K.69, F:K.184, F:K.184, F:E.265, F:H.315 Water bridges: F:Y.152, F:Y.152 Salt bridges: F:K.182, F:K.184, F:K.184, F:H.315 LGT.21: 13 residues within 4Å: Chain G: M.44, K.69, F.158, K.182, K.184, D.213, N.215, E.239, E.265, H.315, E.335, F.337 Ligands: MG.19 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:K.69, G:K.69, G:K.184, G:E.265, G:H.315 Salt bridges: G:K.182, G:K.184, G:K.184, G:H.315 LGT.24: 12 residues within 4Å: Chain H: K.69, K.182, K.184, D.213, N.215, E.239, E.265, H.315, E.335, F.337, W.339 Ligands: MG.22 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:K.69, H:D.213, H:D.213, H:E.265, H:H.315 Water bridges: H:E.240 Salt bridges: H:K.69, H:K.182, H:K.184, H:H.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of L-Talarate dehydratase from Polaromonas sp. JS666 complexed with Mg and L-glucarate. To be Published

Release Date

2008-03-04

Peptides

Mandelate racemase/muconate lactonizing enzyme: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Mandelate racemase/muconate lactonizing enzyme

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