SMTL ID : 4fp1.1

P. putida mandelate racemase co-crystallized with 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl) propionic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: K.188, K.190, D.219, E.245, E.271 Ligands: BFM.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.219, A:E.245, H2O.9, H2O.9, H2O.9 MG.3: 5 residues within 4Å: Chain B: K.190, D.219, E.245, E.271 Ligands: BFM.4 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.219, B:E.245, B:E.271, H2O.17, H2O.17, H2O.17 MG.5: 6 residues within 4Å: Chain C: K.188, K.190, D.219, E.245, E.271 Ligands: BFM.6 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.219, C:E.245, H2O.26, H2O.27, H2O.27 MG.7: 5 residues within 4Å: Chain D: K.190, D.219, E.245, E.271 Ligands: BFM.8 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.219, D:E.245, D:E.271, H2O.34, H2O.34, H2O.35 MG.9: 6 residues within 4Å: Chain E: K.188, K.190, D.219, E.245, E.271 Ligands: BFM.10 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.219, E:E.245, H2O.44, H2O.44, H2O.44 MG.11: 5 residues within 4Å: Chain F: K.190, D.219, E.245, E.271 Ligands: BFM.12 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.219, F:E.245, F:E.271, H2O.51, H2O.51, H2O.52 MG.13: 6 residues within 4Å: Chain G: K.188, K.190, D.219, E.245, E.271 Ligands: BFM.14 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.219, G:E.245, H2O.61, H2O.61, H2O.61 MG.15: 5 residues within 4Å: Chain H: K.190, D.219, E.245, E.271 Ligands: BFM.16 6 PLIP interactions: 3 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.219, H:E.245, H:E.271, H2O.69, H2O.69, H2O.69

8 x BFM: 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)propanoic acid(Non-covalent)

BFM.2: 13 residues within 4Å: Chain A: V.46, T.48, V.53, F.76, Y.78, K.190, N.221, E.271, H.321, L.322, L.343 Chain B: L.117 Ligands: MG.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.221 Water bridges: A:K.190, A:K.190, A:K.190 Salt bridges: A:K.190, A:H.321 BFM.4: 13 residues within 4Å: Chain A: L.117 Chain B: V.46, T.48, V.53, F.76, Y.78, K.190, N.221, E.271, H.321, L.322, L.343 Ligands: MG.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.221, B:E.271 Water bridges: B:K.190, B:K.190, B:K.190, B:K.190 Salt bridges: B:K.190, B:H.321 BFM.6: 13 residues within 4Å: Chain C: V.46, T.48, V.53, F.76, Y.78, K.190, N.221, E.271, H.321, L.322, L.343 Chain D: L.117 Ligands: MG.5 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.221 Water bridges: C:K.190, C:K.190, C:K.190 Salt bridges: C:K.190, C:H.321 BFM.8: 13 residues within 4Å: Chain C: L.117 Chain D: V.46, T.48, V.53, F.76, Y.78, K.190, N.221, E.271, H.321, L.322, L.343 Ligands: MG.7 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.221, D:E.271 Water bridges: D:K.190, D:K.190, D:K.190, D:K.190 Salt bridges: D:K.190, D:H.321 BFM.10: 13 residues within 4Å: Chain E: V.46, T.48, V.53, F.76, Y.78, K.190, N.221, E.271, H.321, L.322, L.343 Chain F: L.117 Ligands: MG.9 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.221 Water bridges: E:K.190, E:K.190, E:K.190 Salt bridges: E:K.190, E:H.321 BFM.12: 13 residues within 4Å: Chain E: L.117 Chain F: V.46, T.48, V.53, F.76, Y.78, K.190, N.221, E.271, H.321, L.322, L.343 Ligands: MG.11 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:N.221, F:E.271 Water bridges: F:K.190, F:K.190, F:K.190, F:K.190 Salt bridges: F:K.190, F:H.321 BFM.14: 13 residues within 4Å: Chain G: V.46, T.48, V.53, F.76, Y.78, K.190, N.221, E.271, H.321, L.322, L.343 Chain H: L.117 Ligands: MG.13 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:N.221 Water bridges: G:K.190, G:K.190, G:K.190 Salt bridges: G:K.190, G:H.321 BFM.16: 13 residues within 4Å: Chain G: L.117 Chain H: V.46, T.48, V.53, F.76, Y.78, K.190, N.221, E.271, H.321, L.322, L.343 Ligands: MG.15 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:N.221, H:E.271 Water bridges: H:K.190, H:K.190, H:K.190, H:K.190 Salt bridges: H:K.190, H:H.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagar, M. et al., Potent inhibition of mandelate racemase by a fluorinated substrate-product analogue with a novel binding mode. Biochemistry (2014)

Release Date

2013-06-26

Peptides

Mandelate racemase: 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

Mandelate racemase

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