SMTL ID : 4x2p.1

P. putida mandelate racemase in complex with 3-hydroxypyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-octamer

Ligands

8 x 3PY: 3-HYDROXYPYRUVIC ACID(Covalent)

3PY.1: 11 residues within 4Å: Chain A: S.163, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.190 Hydrogen bonds: A:S.163, A:D.219, A:D.219 Water bridges: A:E.271 Salt bridges: A:K.188, A:K.190, A:H.321 3PY.3: 11 residues within 4Å: Chain B: S.163, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:K.190 Hydrogen bonds: B:S.163, B:D.219, B:D.219 Water bridges: B:E.271 Salt bridges: B:K.188, B:K.190, B:H.321 3PY.5: 11 residues within 4Å: Chain C: S.163, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.6 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:K.190 Hydrogen bonds: C:S.163, C:D.219, C:D.219 Water bridges: C:E.271 Salt bridges: C:K.188, C:K.190, C:H.321 3PY.7: 11 residues within 4Å: Chain D: S.163, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.8 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:K.190 Hydrogen bonds: D:S.163, D:D.219, D:D.219 Water bridges: D:E.271 Salt bridges: D:K.188, D:K.190, D:H.321 3PY.9: 11 residues within 4Å: Chain E: S.163, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.10 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:K.190 Hydrogen bonds: E:S.163, E:D.219 Water bridges: E:E.271, E:E.271 Salt bridges: E:K.188, E:K.190, E:H.321 3PY.11: 11 residues within 4Å: Chain F: S.163, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:K.190 Hydrogen bonds: F:S.163, F:D.219 Water bridges: F:E.271, F:E.271 Salt bridges: F:K.188, F:K.190, F:H.321 3PY.13: 11 residues within 4Å: Chain G: S.163, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.14 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:K.190 Hydrogen bonds: G:S.163, G:D.219 Water bridges: G:E.271, G:E.271 Salt bridges: G:K.188, G:K.190, G:H.321 3PY.15: 11 residues within 4Å: Chain H: S.163, K.188, K.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.16 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:K.190 Hydrogen bonds: H:S.163, H:D.219 Water bridges: H:E.245, H:E.271, H:E.271 Salt bridges: H:K.188, H:K.190, H:H.321

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.188, D.219, N.221, E.245, E.271 Ligands: 3PY.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.219, A:E.245, A:E.271, H2O.9, H2O.10 MG.4: 6 residues within 4Å: Chain B: K.188, D.219, N.221, E.245, E.271 Ligands: 3PY.3 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.219, B:E.245, B:E.271, H2O.21, H2O.22 MG.6: 6 residues within 4Å: Chain C: K.188, D.219, N.221, E.245, E.271 Ligands: 3PY.5 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.219, C:E.245, C:E.271, H2O.32, H2O.33 MG.8: 6 residues within 4Å: Chain D: K.188, D.219, N.221, E.245, E.271 Ligands: 3PY.7 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.219, D:E.245, D:E.271, H2O.43, H2O.44 MG.10: 6 residues within 4Å: Chain E: K.188, D.219, N.221, E.245, E.271 Ligands: 3PY.9 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.219, E:E.245, E:E.271, H2O.55, H2O.56 MG.12: 6 residues within 4Å: Chain F: K.188, D.219, N.221, E.245, E.271 Ligands: 3PY.11 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.219, F:E.245, F:E.271, H2O.66, H2O.67 MG.14: 6 residues within 4Å: Chain G: K.188, D.219, N.221, E.245, E.271 Ligands: 3PY.13 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.219, G:E.245, G:E.271, H2O.78, H2O.79 MG.16: 6 residues within 4Å: Chain H: K.188, D.219, N.221, E.245, E.271 Ligands: 3PY.15 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.219, H:E.245, H:E.271, H2O.89, H2O.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagar, M. et al., Inactivation of Mandelate Racemase by 3-Hydroxypyruvate Reveals a Potential Mechanistic Link between Enzyme Superfamilies. Biochemistry (2015)

Release Date

2015-10-14

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

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