SMTL ID : 7mqx.1

P. putida mandelate racemase forms an oxobenzoxaborole adduct with 2-formylphenylboronic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.190, D.219, E.245, E.271 Ligands: ZMD.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.219, A:E.245, A:E.271, H2O.1, H2O.1 MG.6: 6 residues within 4Å: Chain B: K.190, D.219, N.221, E.245, E.271 Ligands: ZMD.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.219, B:E.245, B:E.271, H2O.12, H2O.12 MG.12: 6 residues within 4Å: Chain C: K.188, K.190, D.219, E.245, E.271 Ligands: ZMD.13 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.219, C:E.245, C:E.271, H2O.22, H2O.22 MG.16: 5 residues within 4Å: Chain D: K.190, D.219, E.245, E.271 Ligands: ZMD.17 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.219, D:E.245, D:E.271, H2O.32, H2O.33 MG.21: 5 residues within 4Å: Chain E: K.190, D.219, E.245, E.271 Ligands: ZMD.22 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.219, E:E.245, E:E.271, H2O.42, H2O.43 MG.26: 6 residues within 4Å: Chain F: K.188, K.190, D.219, E.245, E.271 Ligands: ZMD.27 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.219, F:E.245, F:E.271, H2O.53, H2O.53 MG.31: 5 residues within 4Å: Chain G: K.190, D.219, E.245, E.271 Ligands: ZMD.32 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.219, G:E.245, G:E.271, H2O.63, H2O.64 MG.36: 5 residues within 4Å: Chain H: K.190, D.219, E.245, E.271 Ligands: ZMD.37 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.219, H:E.245, H:E.271, H2O.73, H2O.73

8 x ZMD: (3S)-2,1-benzoxaborole-1,3(3H)-diol(Covalent)

ZMD.2: 14 residues within 4Å: Chain A: V.46, F.76, Y.78, K.188, K.190, D.219, N.221, E.271, H.321, L.322, E.341, L.343 Chain B: L.117 Ligands: MG.1 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.117, A:V.46, A:F.76, A:Y.78 Hydrogen bonds: A:D.219, A:N.221, A:E.271 Water bridges: A:K.188 Salt bridges: A:K.188, A:K.190, A:H.321 pi-Stacking: A:H.321 ZMD.7: 14 residues within 4Å: Chain A: L.117 Chain B: V.46, F.76, Y.78, K.188, K.190, D.219, N.221, E.271, H.321, L.322, E.341, L.343 Ligands: MG.6 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.46, B:F.76, B:Y.78, A:L.117 Hydrogen bonds: B:D.219, B:N.221, B:E.271 Water bridges: B:K.188, B:K.188 Salt bridges: B:K.188, B:K.190, B:H.321 pi-Stacking: B:H.321 ZMD.13: 14 residues within 4Å: Chain C: V.46, F.76, Y.78, K.188, K.190, D.219, N.221, E.271, H.321, L.322, E.341, L.343 Chain D: L.117 Ligands: MG.12 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.46, C:F.76, C:Y.78, D:L.117 Hydrogen bonds: C:D.219, C:N.221, C:E.271 Water bridges: C:K.188, C:K.188, C:K.188 Salt bridges: C:K.188, C:K.190, C:H.321 pi-Stacking: C:H.321 ZMD.17: 14 residues within 4Å: Chain C: L.117 Chain D: V.46, T.48, V.53, K.188, K.190, D.219, N.221, E.271, H.321, L.322, E.341, L.343 Ligands: MG.16 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.46, D:T.48, D:V.53, C:L.117 Hydrogen bonds: D:N.221, D:E.271 Water bridges: D:K.190, D:K.190 Salt bridges: D:K.188, D:K.190, D:H.321 pi-Stacking: D:H.321 ZMD.22: 15 residues within 4Å: Chain E: V.46, T.48, F.76, Y.78, K.188, K.190, D.219, N.221, E.271, H.321, L.322, E.341, L.343 Chain F: L.117 Ligands: MG.21 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:V.46, E:T.48, E:F.76, E:Y.78, F:L.117 Hydrogen bonds: E:D.219, E:N.221, E:E.271 Salt bridges: E:K.188, E:K.190, E:H.321 ZMD.27: 12 residues within 4Å: Chain F: V.46, T.48, K.188, K.190, D.219, N.221, E.271, H.321, L.322, E.341, L.343 Ligands: MG.26 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:V.46, F:T.48 Hydrogen bonds: F:N.221, F:E.271 Water bridges: F:K.188, F:K.190, F:E.245 Salt bridges: F:K.188, F:K.190, F:H.321 pi-Stacking: F:H.321 ZMD.32: 14 residues within 4Å: Chain G: V.46, F.76, Y.78, K.188, K.190, D.219, N.221, E.271, H.321, L.322, E.341, L.343 Chain H: L.117 Ligands: MG.31 10 PLIP interactions: 1 interactions with chain H, 9 interactions with chain G Hydrophobic interactions: H:L.117, G:V.46, G:F.76, G:Y.78 Hydrogen bonds: G:N.221, G:E.271 Salt bridges: G:K.188, G:K.190, G:H.321 pi-Stacking: G:H.321 ZMD.37: 13 residues within 4Å: Chain G: L.117 Chain H: V.46, Y.78, K.188, K.190, D.219, N.221, E.271, H.321, L.322, E.341, L.343 Ligands: MG.36 12 PLIP interactions: 1 interactions with chain G, 11 interactions with chain H Hydrophobic interactions: G:L.117, H:V.46, H:Y.78 Hydrogen bonds: H:D.219, H:N.221, H:E.271 Water bridges: H:K.190, H:K.190 Salt bridges: H:K.188, H:K.190, H:H.321 pi-Stacking: H:H.321

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: Y.44, D.162, H.164, R.175, T.178, R.342 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: V.105, S.106 Chain H: R.156, A.332, A.333, T.334, P.335 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: G.192, Y.193, S.223, L.224, R.232 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain B: Y.44, D.162, H.164, R.175, T.178, R.342 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain B: V.105, S.106, A.109 Chain C: R.156, A.332, T.334, P.335 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain B: R.156, A.332, A.333, T.334, P.335 Chain C: V.105, S.106, A.109 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain B: A.49, G.192, Y.193, S.223, L.224, R.232 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain C: Y.44, D.162, H.164, R.175, T.178, L.182, R.342 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain C: A.49, G.192, Y.193, S.223, L.224, R.232 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain D: Y.44, D.162, H.164, R.175, T.178, R.342 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain D: R.156, A.332, T.334, P.335 Chain E: V.105, S.106 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain D: A.49, G.192, Y.193, S.223, L.224, R.232 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain E: Y.44, D.162, H.164, R.175, T.178, R.342 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain D: V.105, S.106, A.109 Chain E: R.156, A.332, A.333, T.334, P.335 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain E: A.49, G.192, Y.193, S.223, L.224, R.232 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain F: Y.44, D.162, H.164, R.175, T.178, L.182, R.342 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain F: S.106 Chain G: R.156, A.332, A.333, T.334, P.335 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain F: A.49, G.192, Y.193, S.223, L.224, R.232 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain G: Y.44, D.162, H.164, R.175, T.178, R.342 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain F: R.156, A.332, A.333, T.334, P.335 Chain G: V.105, S.106 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain G: G.192, Y.193, S.223, L.224, R.232 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain H: Y.44, D.162, H.164, R.175, T.178, R.342 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain A: R.156, A.332, A.333, T.334, P.335 Chain H: V.105, S.106 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain H: A.49, G.192, Y.193, S.223, L.224, R.232 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Douglas, C.D. et al., Slow-Onset, Potent Inhibition of Mandelate Racemase by 2-Formylphenylboronic Acid. An Unexpected Adduct Clasps the Catalytic Machinery. Biochemistry (2021)

Release Date

2021-08-11

Peptides

Mandelate racemase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Mandelate racemase

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