SMTL ID : 6vim.1

P. putida mandelate racemase co-crystallized with phenylboronic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.219, E.245, E.271 Ligands: PBC.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.1 MG.7: 7 residues within 4Å: Chain B: K.188, D.219, N.221, E.245, E.271, H.321 Ligands: PBC.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.219, B:E.245, B:E.271, H2O.18 MG.11: 4 residues within 4Å: Chain C: D.219, E.245, E.271 Ligands: PBC.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.219, C:E.245, C:E.271, H2O.33 MG.15: 8 residues within 4Å: Chain D: K.188, K.190, D.219, N.221, E.245, E.271, H.321 Ligands: PBC.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.219, D:E.245, D:E.271, H2O.50 MG.17: 6 residues within 4Å: Chain E: K.190, D.219, N.221, E.245, E.271 Ligands: PBC.18 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.219, E:E.245, E:E.271, H2O.66 MG.21: 6 residues within 4Å: Chain F: D.219, N.221, E.245, E.271, H.321 Ligands: PBC.22 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.219, F:E.245, F:E.271, H2O.82 MG.25: 6 residues within 4Å: Chain G: K.188, D.219, N.221, E.245, E.271 Ligands: PBC.26 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.219, G:E.245, G:E.271, H2O.98 MG.29: 5 residues within 4Å: Chain H: D.219, N.221, E.245, E.271 Ligands: PBC.30 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.219, H:E.245, H:E.271, H2O.114

8 x PBC: PHENYL BORONIC ACID(Non-covalent)(Covalent)

PBC.2: 13 residues within 4Å: Chain A: V.46, Y.78, K.188, K.190, D.219, N.221, E.245, E.271, H.321, L.322, E.341, L.343 Ligands: MG.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.46, A:Y.78, A:L.322, A:L.343 Hydrogen bonds: A:K.188, A:K.190, A:D.219, A:N.221 PBC.8: 12 residues within 4Å: Chain B: V.46, K.188, K.190, D.219, N.221, E.245, E.271, H.321, L.322, E.341, L.343 Ligands: MG.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.46, B:L.322, B:L.343 Hydrogen bonds: B:K.188, B:K.190, B:K.190, B:D.219, B:N.221 PBC.12: 13 residues within 4Å: Chain C: V.46, Y.78, K.188, K.190, D.219, N.221, E.245, E.271, H.321, L.322, E.341, L.343 Ligands: MG.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.46, C:Y.78, C:L.322, C:L.343 Hydrogen bonds: C:K.188, C:K.190, C:D.219, C:N.221 PBC.16: 13 residues within 4Å: Chain D: V.46, Y.78, K.188, K.190, D.219, N.221, E.245, E.271, H.321, L.322, E.341, L.343 Ligands: MG.15 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:V.46, D:Y.78, D:L.322, D:L.343 Hydrogen bonds: D:K.188, D:K.190, D:K.190, D:K.190, D:N.221, D:E.245 PBC.18: 14 residues within 4Å: Chain E: V.46, F.76, Y.78, K.188, K.190, D.219, N.221, E.245, E.271, H.321, L.322, E.341, L.343 Ligands: MG.17 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:V.46, E:F.76, E:Y.78, E:L.322, E:L.343 Hydrogen bonds: E:K.188, E:K.190, E:N.221 PBC.22: 12 residues within 4Å: Chain F: V.46, K.188, K.190, D.219, N.221, E.245, E.271, H.321, L.322, E.341, L.343 Ligands: MG.21 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:V.46, F:L.322, F:L.343 Hydrogen bonds: F:K.188, F:K.190, F:K.190, F:N.221 PBC.26: 14 residues within 4Å: Chain G: V.46, F.76, Y.78, K.188, K.190, D.219, N.221, E.245, E.271, H.321, L.322, E.341, L.343 Ligands: MG.25 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:V.46, G:F.76, G:Y.78, G:L.322, G:L.343 Hydrogen bonds: G:K.188, G:K.188, G:K.190, G:N.221 Water bridges: G:E.341 PBC.30: 13 residues within 4Å: Chain H: V.46, Y.78, K.188, K.190, D.219, N.221, E.245, E.271, H.321, L.322, E.341, L.343 Ligands: MG.29 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:V.46, H:Y.78, H:L.322, H:L.343 Hydrogen bonds: H:K.188, H:K.190, H:D.219, H:N.221

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

EDO.3: 8 residues within 4Å: Chain A: V.105, S.106, A.109 Chain H: R.156, A.332, A.333, T.334, P.335 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:R.156, H:R.156, H:T.334, A:S.106 Water bridges: H:N.154 EDO.4: 6 residues within 4Å: Chain A: Y.44, D.162, H.164, R.175, T.178, R.342 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.175, A:R.175, A:R.342 EDO.5: 7 residues within 4Å: Chain A: R.156, A.332, A.333, T.334, P.335 Chain H: V.105, S.106 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain H Hydrogen bonds: A:R.156, A:R.156, A:T.334, H:S.106 Water bridges: A:N.154 EDO.6: 5 residues within 4Å: Chain A: K.149 Chain H: E.27, V.28, L.102, L.139 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain A Hydrogen bonds: H:E.27, H:V.28, A:K.149 Water bridges: A:T.145, A:T.145 EDO.9: 6 residues within 4Å: Chain B: A.49, G.192, Y.193, S.223, L.224, R.232 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.223, B:S.223 Water bridges: B:P.194, B:R.232 EDO.10: 7 residues within 4Å: Chain B: R.156, A.332, A.333, T.334, P.335 Chain C: V.105, S.106 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.156, B:R.156, B:T.334, C:S.106 Water bridges: B:N.154 EDO.13: 7 residues within 4Å: Chain C: Y.44, D.162, H.164, R.175, T.178, L.182, R.342 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.175, C:R.175, C:R.342 EDO.14: 6 residues within 4Å: Chain C: A.49, G.192, Y.193, S.223, L.224, R.232 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.223, C:S.223 Water bridges: C:R.232 EDO.19: 7 residues within 4Å: Chain E: Y.44, D.162, H.164, R.175, T.178, L.182, R.342 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.175, E:R.175, E:R.342 EDO.20: 4 residues within 4Å: Chain E: L.42, A.43, Y.44, L.343 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:A.43 Water bridges: E:P.41, E:R.175, E:R.175, E:D.344, E:D.344 EDO.23: 6 residues within 4Å: Chain F: A.49, G.192, Y.193, S.223, L.224, R.232 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.223, F:S.223, F:R.232 Water bridges: F:P.194 EDO.24: 5 residues within 4Å: Chain F: Y.44, D.162, H.164, R.175, R.342 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.175, F:R.175, F:R.342 EDO.27: 6 residues within 4Å: Chain G: Y.44, D.162, H.164, R.175, T.178, R.342 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.175, G:R.175, G:R.342 EDO.28: 6 residues within 4Å: Chain G: A.49, G.192, Y.193, S.223, L.224, R.232 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:G.192, G:S.223, G:R.232 EDO.31: 6 residues within 4Å: Chain H: A.49, G.192, Y.193, S.223, L.224, R.232 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:S.223, H:S.223 Water bridges: H:R.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, A.N. et al., Potent Inhibition of Mandelate Racemase by Boronic Acids: Boron as a Mimic of a Carbon Acid Center. Biochemistry (2020)

Release Date

2020-08-05

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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