SMTL ID : 1mdl.1

MANDELATE RACEMASE MUTANT K166R CO-CRYSTALLIZED WITH (R)-MANDELATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.195, E.221, E.247 Ligands: SMN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.195, A:E.221, A:E.247, H2O.3 MG.4: 4 residues within 4Å: Chain B: D.195, E.221, E.247 Ligands: SMN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.195, B:E.221, B:E.247, H2O.10 MG.7: 4 residues within 4Å: Chain C: D.195, E.221, E.247 Ligands: SMN.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.195, C:E.221, C:E.247, H2O.16 MG.10: 4 residues within 4Å: Chain D: D.195, E.221, E.247 Ligands: SMN.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.195, D:E.221, D:E.247, H2O.23 MG.13: 4 residues within 4Å: Chain E: D.195, E.221, E.247 Ligands: SMN.15 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.195, E:E.221, E:E.247, H2O.29 MG.16: 4 residues within 4Å: Chain F: D.195, E.221, E.247 Ligands: SMN.18 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.195, F:E.221, F:E.247, H2O.36 MG.19: 4 residues within 4Å: Chain G: D.195, E.221, E.247 Ligands: SMN.21 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.195, G:E.221, G:E.247, H2O.43 MG.22: 4 residues within 4Å: Chain H: D.195, E.221, E.247 Ligands: SMN.24 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.195, H:E.221, H:E.247, H2O.49

8 x RMN: (R)-MANDELIC ACID(Non-covalent)

RMN.2: 10 residues within 4Å: Chain A: L.18, V.22, T.24, V.29, T.31, F.52, Y.54, R.166 Chain B: L.93 Ligands: SMN.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.18, A:V.22, A:V.29 Water bridges: A:Y.54, A:Y.54 Salt bridges: A:R.166 pi-Stacking: A:F.52 RMN.5: 10 residues within 4Å: Chain A: L.93 Chain B: L.18, V.22, T.24, V.29, T.31, F.52, Y.54, R.166 Ligands: SMN.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.18, B:V.22, B:V.29 Water bridges: B:Y.54, B:Y.54 Salt bridges: B:R.166 pi-Stacking: B:F.52 RMN.8: 10 residues within 4Å: Chain C: L.18, V.22, T.24, V.29, T.31, F.52, Y.54, R.166 Chain D: L.93 Ligands: SMN.9 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.18, C:V.22, C:V.29 Water bridges: C:Y.54, C:Y.54 Salt bridges: C:R.166 pi-Stacking: C:F.52 RMN.11: 10 residues within 4Å: Chain C: L.93 Chain D: L.18, V.22, T.24, V.29, T.31, F.52, Y.54, R.166 Ligands: SMN.12 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.18, D:V.22, D:V.29 Water bridges: D:Y.54, D:Y.54 Salt bridges: D:R.166 pi-Stacking: D:F.52 RMN.14: 10 residues within 4Å: Chain E: L.18, V.22, T.24, V.29, T.31, F.52, Y.54, R.166 Chain F: L.93 Ligands: SMN.15 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.18, E:V.22, E:V.29 Water bridges: E:Y.54, E:Y.54 Salt bridges: E:R.166 pi-Stacking: E:F.52 RMN.17: 10 residues within 4Å: Chain E: L.93 Chain F: L.18, V.22, T.24, V.29, T.31, F.52, Y.54, R.166 Ligands: SMN.18 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:L.18, F:V.22, F:V.29 Water bridges: F:Y.54, F:Y.54 Salt bridges: F:R.166 pi-Stacking: F:F.52 RMN.20: 10 residues within 4Å: Chain G: L.18, V.22, T.24, V.29, T.31, F.52, Y.54, R.166 Chain H: L.93 Ligands: SMN.21 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:L.18, G:V.22, G:V.29 Water bridges: G:Y.54, G:Y.54 Salt bridges: G:R.166 pi-Stacking: G:F.52 RMN.23: 10 residues within 4Å: Chain G: L.93 Chain H: L.18, V.22, T.24, V.29, T.31, F.52, Y.54, R.166 Ligands: SMN.24 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:L.18, H:V.22, H:V.29 Water bridges: H:Y.54, H:Y.54 Salt bridges: H:R.166 pi-Stacking: H:F.52

8 x SMN: (S)-MANDELIC ACID(Non-covalent)

SMN.3: 14 residues within 4Å: Chain A: F.52, Y.54, S.139, K.164, R.166, D.195, N.197, E.221, E.247, M.268, H.297, E.317 Ligands: MG.1, RMN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.52, A:Y.54 Hydrogen bonds: A:S.139, A:D.195, A:N.197 Water bridges: A:R.166, A:R.166 Salt bridges: A:K.164, A:H.297 pi-Stacking: A:H.297 SMN.6: 14 residues within 4Å: Chain B: F.52, Y.54, S.139, K.164, R.166, D.195, N.197, E.221, E.247, M.268, H.297, E.317 Ligands: MG.4, RMN.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.52, B:Y.54 Hydrogen bonds: B:S.139, B:N.197 Water bridges: B:R.166, B:N.197, B:E.221, B:E.221 Salt bridges: B:K.164, B:H.297 pi-Stacking: B:H.297 SMN.9: 14 residues within 4Å: Chain C: F.52, Y.54, S.139, K.164, R.166, D.195, N.197, E.221, E.247, M.268, H.297, E.317 Ligands: MG.7, RMN.8 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.52, C:Y.54 Hydrogen bonds: C:S.139, C:N.197 Water bridges: C:R.166, C:N.197, C:E.221, C:E.221 Salt bridges: C:K.164, C:H.297 pi-Stacking: C:H.297 SMN.12: 14 residues within 4Å: Chain D: F.52, Y.54, S.139, K.164, R.166, D.195, N.197, E.221, E.247, M.268, H.297, E.317 Ligands: MG.10, RMN.11 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.52, D:Y.54 Hydrogen bonds: D:S.139, D:D.195, D:N.197 Water bridges: D:R.166, D:R.166 Salt bridges: D:K.164, D:H.297 pi-Stacking: D:H.297 SMN.15: 14 residues within 4Å: Chain E: F.52, Y.54, S.139, K.164, R.166, D.195, N.197, E.221, E.247, M.268, H.297, E.317 Ligands: MG.13, RMN.14 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.52, E:Y.54 Hydrogen bonds: E:S.139, E:D.195, E:N.197 Water bridges: E:R.166, E:R.166 Salt bridges: E:K.164, E:H.297 pi-Stacking: E:H.297 SMN.18: 14 residues within 4Å: Chain F: F.52, Y.54, S.139, K.164, R.166, D.195, N.197, E.221, E.247, M.268, H.297, E.317 Ligands: MG.16, RMN.17 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:F.52, F:Y.54 Hydrogen bonds: F:S.139, F:N.197 Water bridges: F:R.166, F:N.197, F:E.221, F:E.221 Salt bridges: F:K.164, F:H.297 pi-Stacking: F:H.297 SMN.21: 14 residues within 4Å: Chain G: F.52, Y.54, S.139, K.164, R.166, D.195, N.197, E.221, E.247, M.268, H.297, E.317 Ligands: MG.19, RMN.20 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:F.52, G:Y.54 Hydrogen bonds: G:S.139, G:N.197 Water bridges: G:R.166, G:N.197, G:E.221, G:E.221 Salt bridges: G:K.164, G:H.297 pi-Stacking: G:H.297 SMN.24: 14 residues within 4Å: Chain H: F.52, Y.54, S.139, K.164, R.166, D.195, N.197, E.221, E.247, M.268, H.297, E.317 Ligands: MG.22, RMN.23 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:F.52, H:Y.54 Hydrogen bonds: H:S.139, H:D.195, H:N.197 Water bridges: H:R.166, H:R.166 Salt bridges: H:K.164, H:H.297 pi-Stacking: H:H.297

Links

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Citation

Kallarakal, A.T. et al., Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the K166R mutant. Biochemistry (1995)

Release Date

1996-10-14

Peptides

MANDELATE RACEMASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

MANDELATE RACEMASE