SMTL ID : 4hnc.1

P. putida C92S/K166C/C264S mandelate racemase co-crystallized with benzilic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-16-mer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.188, D.219, E.245, E.271 Ligands: 0UT.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.219, A:E.245, A:E.271, H2O.11 MG.3: 5 residues within 4Å: Chain B: K.188, D.219, E.245, E.271 Ligands: 0UT.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.219, B:E.245, B:E.271, H2O.20 MG.5: 5 residues within 4Å: Chain C: K.188, D.219, E.245, E.271 Ligands: 0UT.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.219, C:E.245, C:E.271, H2O.30 MG.7: 5 residues within 4Å: Chain D: K.188, D.219, E.245, E.271 Ligands: 0UT.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.219, D:E.245, D:E.271, H2O.39 MG.9: 5 residues within 4Å: Chain E: K.188, D.219, E.245, E.271 Ligands: 0UT.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.219, E:E.245, E:E.271, H2O.49 MG.11: 5 residues within 4Å: Chain F: K.188, D.219, E.245, E.271 Ligands: 0UT.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.219, F:E.245, F:E.271, H2O.58 MG.13: 5 residues within 4Å: Chain G: K.188, D.219, E.245, E.271 Ligands: 0UT.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.219, G:E.245, G:E.271, H2O.69 MG.15: 5 residues within 4Å: Chain H: K.188, D.219, E.245, E.271 Ligands: 0UT.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.219, H:E.245, H:E.271, H2O.78 MG.17: 5 residues within 4Å: Chain I: K.188, D.219, E.245, E.271 Ligands: 0UT.18 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.219, I:E.245, I:E.271, H2O.88 MG.19: 5 residues within 4Å: Chain J: K.188, D.219, E.245, E.271 Ligands: 0UT.20 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.219, J:E.245, J:E.271, H2O.97 MG.21: 5 residues within 4Å: Chain K: K.188, D.219, E.245, E.271 Ligands: 0UT.22 4 PLIP interactions: 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.219, K:E.245, K:E.271, H2O.108 MG.23: 5 residues within 4Å: Chain L: K.188, D.219, E.245, E.271 Ligands: 0UT.24 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:D.219, L:E.245, L:E.271, H2O.117 MG.25: 5 residues within 4Å: Chain M: K.188, D.219, E.245, E.271 Ligands: 0UT.26 4 PLIP interactions: 3 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:D.219, M:E.245, M:E.271, H2O.127 MG.27: 5 residues within 4Å: Chain N: K.188, D.219, E.245, E.271 Ligands: 0UT.28 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:D.219, N:E.245, N:E.271, H2O.136 MG.29: 5 residues within 4Å: Chain O: K.188, D.219, E.245, E.271 Ligands: 0UT.30 4 PLIP interactions: 3 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:D.219, O:E.245, O:E.271, H2O.146 MG.31: 5 residues within 4Å: Chain P: K.188, D.219, E.245, E.271 Ligands: 0UT.32 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:D.219, P:E.245, P:E.271, H2O.155

16 x 0UT: hydroxy(diphenyl)acetic acid(Non-covalent)

0UT.2: 15 residues within 4Å: Chain A: F.76, Y.78, H.164, K.188, C.190, D.219, N.221, E.245, E.271, M.292, H.321, L.322, E.341, L.343 Ligands: MG.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.76, A:Y.78, A:L.322, A:L.343 Hydrogen bonds: A:E.271 Salt bridges: A:K.188, A:H.321 pi-Stacking: A:H.321 0UT.4: 12 residues within 4Å: Chain B: F.76, H.164, K.188, C.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.76 Hydrogen bonds: B:E.271 Salt bridges: B:K.188, B:H.321 pi-Stacking: B:H.321 0UT.6: 15 residues within 4Å: Chain C: F.76, Y.78, H.164, K.188, C.190, D.219, N.221, E.245, E.271, M.292, H.321, L.322, E.341, L.343 Ligands: MG.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.76, C:Y.78, C:L.322, C:L.343 Hydrogen bonds: C:E.271 Salt bridges: C:K.188, C:H.321 pi-Stacking: C:H.321 0UT.8: 12 residues within 4Å: Chain D: F.76, H.164, K.188, C.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.7 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.76 Hydrogen bonds: D:E.271 Salt bridges: D:K.188, D:H.321 pi-Stacking: D:H.321 0UT.10: 15 residues within 4Å: Chain E: F.76, Y.78, H.164, K.188, C.190, D.219, N.221, E.245, E.271, M.292, H.321, L.322, E.341, L.343 Ligands: MG.9 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.76, E:Y.78, E:L.322, E:L.343 Hydrogen bonds: E:E.271 Salt bridges: E:K.188, E:H.321 pi-Stacking: E:H.321 0UT.12: 12 residues within 4Å: Chain F: F.76, H.164, K.188, C.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.11 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.76 Hydrogen bonds: F:E.271 Salt bridges: F:K.188, F:H.321 pi-Stacking: F:H.321 0UT.14: 15 residues within 4Å: Chain G: F.76, Y.78, H.164, K.188, C.190, D.219, N.221, E.245, E.271, M.292, H.321, L.322, E.341, L.343 Ligands: MG.13 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:F.76, G:Y.78, G:L.322, G:L.343 Hydrogen bonds: G:E.271 Salt bridges: G:K.188, G:H.321 pi-Stacking: G:H.321 0UT.16: 12 residues within 4Å: Chain H: F.76, H.164, K.188, C.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.15 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:F.76 Hydrogen bonds: H:D.219, H:E.245, H:E.271 Salt bridges: H:K.188, H:H.321 pi-Stacking: H:H.321 0UT.18: 15 residues within 4Å: Chain I: F.76, Y.78, H.164, K.188, C.190, D.219, N.221, E.245, E.271, M.292, H.321, L.322, E.341, L.343 Ligands: MG.17 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:F.76, I:Y.78, I:L.322, I:L.343 Hydrogen bonds: I:E.271 Salt bridges: I:K.188, I:H.321 pi-Stacking: I:H.321 0UT.20: 12 residues within 4Å: Chain J: F.76, H.164, K.188, C.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.19 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:F.76 Hydrogen bonds: J:E.271 Salt bridges: J:K.188, J:H.321 pi-Stacking: J:H.321 0UT.22: 15 residues within 4Å: Chain K: F.76, Y.78, H.164, K.188, C.190, D.219, N.221, E.245, E.271, M.292, H.321, L.322, E.341, L.343 Ligands: MG.21 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:F.76, K:Y.78, K:L.322, K:L.343 Hydrogen bonds: K:E.271 Salt bridges: K:K.188, K:H.321 pi-Stacking: K:H.321 0UT.24: 12 residues within 4Å: Chain L: F.76, H.164, K.188, C.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.23 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:F.76 Hydrogen bonds: L:E.271 Salt bridges: L:K.188, L:H.321 pi-Stacking: L:H.321 0UT.26: 15 residues within 4Å: Chain M: F.76, Y.78, H.164, K.188, C.190, D.219, N.221, E.245, E.271, M.292, H.321, L.322, E.341, L.343 Ligands: MG.25 8 PLIP interactions: 8 interactions with chain M Hydrophobic interactions: M:F.76, M:Y.78, M:L.322, M:L.343 Hydrogen bonds: M:E.271 Salt bridges: M:K.188, M:H.321 pi-Stacking: M:H.321 0UT.28: 12 residues within 4Å: Chain N: F.76, H.164, K.188, C.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.27 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:F.76 Hydrogen bonds: N:E.271 Salt bridges: N:K.188, N:H.321 pi-Stacking: N:H.321 0UT.30: 15 residues within 4Å: Chain O: F.76, Y.78, H.164, K.188, C.190, D.219, N.221, E.245, E.271, M.292, H.321, L.322, E.341, L.343 Ligands: MG.29 8 PLIP interactions: 8 interactions with chain O Hydrophobic interactions: O:F.76, O:Y.78, O:L.322, O:L.343 Hydrogen bonds: O:E.271 Salt bridges: O:K.188, O:H.321 pi-Stacking: O:H.321 0UT.32: 12 residues within 4Å: Chain P: F.76, H.164, K.188, C.190, D.219, N.221, E.245, E.271, H.321, E.341, L.343 Ligands: MG.31 5 PLIP interactions: 5 interactions with chain P Hydrophobic interactions: P:F.76 Hydrogen bonds: P:E.271 Salt bridges: P:K.188, P:H.321 pi-Stacking: P: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

2013-10-30

Peptides

Mandelate racemase: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

M
A

N
B

O
A

P
B

Mandelate racemase