SMTL ID : 4j1o.1

Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-octamer

Ligands

20 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 7 residues within 4Å: Chain A: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: PBE.12 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.216, A:E.241, A:D.264, H2O.1, PBE.12 MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: A.26, S.391 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.391, A:S.391, H2O.2, H2O.11, H2O.14 MG.13: 7 residues within 4Å: Chain B: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: PBE.19 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.216, B:E.241, B:D.264, H2O.14, PBE.19 MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 7 residues within 4Å: Chain C: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: PBE.31 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:D.216, C:E.241, C:D.264, H2O.27, PBE.31 MG.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain C: A.26, S.391 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.391, C:S.391, H2O.29, H2O.38, H2O.40 MG.32: 7 residues within 4Å: Chain D: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: PBE.38 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.216, D:E.241, D:D.264, H2O.41 MG.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.39: 7 residues within 4Å: Chain E: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: PBE.50 5 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: E:D.216, E:E.241, E:D.264, PBE.50, H2O.54 MG.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain E: A.26, S.391 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.391, E:S.391, H2O.55, H2O.64, H2O.67 MG.51: 7 residues within 4Å: Chain F: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: PBE.57 5 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: F:D.216, F:E.241, F:D.264, PBE.57, H2O.67 MG.52: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.58: 7 residues within 4Å: Chain G: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: PBE.69 5 PLIP interactions: 3 interactions with chain G, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: G:D.216, G:E.241, G:D.264, PBE.69, H2O.80 MG.59: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.60: 2 residues within 4Å: Chain G: A.26, S.391 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:S.391, G:S.391, H2O.82, H2O.91, H2O.93 MG.70: 7 residues within 4Å: Chain H: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: PBE.76 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.216, H:E.241, H:D.264, H2O.94 MG.71: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

44 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 3 residues within 4Å: Chain A: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: V.387 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: L.65, A.66, K.136 Ligands: IOD.8 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: A.79, S.81, R.291 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: W.68, K.136 Ligands: IOD.6 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: A.88 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain B: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain B: G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain B: A.88 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain B: A.79, S.81, R.291 Ligand excluded by PLIP IOD.23: 3 residues within 4Å: Chain C: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain C: V.387 Ligand excluded by PLIP IOD.25: 4 residues within 4Å: Chain C: L.65, A.66, K.136 Ligands: IOD.27 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain C: A.79, S.81, R.291 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain C: W.68, K.136 Ligands: IOD.25 Ligand excluded by PLIP IOD.28: 4 residues within 4Å: Chain C: G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.29: 1 residues within 4Å: Chain C: A.88 Ligand excluded by PLIP IOD.34: 3 residues within 4Å: Chain D: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.35: 4 residues within 4Å: Chain D: G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.36: 1 residues within 4Å: Chain D: A.88 Ligand excluded by PLIP IOD.37: 3 residues within 4Å: Chain D: A.79, S.81, R.291 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain E: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.43: 1 residues within 4Å: Chain E: V.387 Ligand excluded by PLIP IOD.44: 4 residues within 4Å: Chain E: L.65, A.66, K.136 Ligands: IOD.46 Ligand excluded by PLIP IOD.45: 3 residues within 4Å: Chain E: A.79, S.81, R.291 Ligand excluded by PLIP IOD.46: 3 residues within 4Å: Chain E: W.68, K.136 Ligands: IOD.44 Ligand excluded by PLIP IOD.47: 4 residues within 4Å: Chain E: G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.48: 1 residues within 4Å: Chain E: A.88 Ligand excluded by PLIP IOD.53: 3 residues within 4Å: Chain F: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.54: 4 residues within 4Å: Chain F: G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.55: 1 residues within 4Å: Chain F: A.88 Ligand excluded by PLIP IOD.56: 3 residues within 4Å: Chain F: A.79, S.81, R.291 Ligand excluded by PLIP IOD.61: 3 residues within 4Å: Chain G: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.62: 1 residues within 4Å: Chain G: V.387 Ligand excluded by PLIP IOD.63: 4 residues within 4Å: Chain G: L.65, A.66, K.136 Ligands: IOD.65 Ligand excluded by PLIP IOD.64: 3 residues within 4Å: Chain G: A.79, S.81, R.291 Ligand excluded by PLIP IOD.65: 3 residues within 4Å: Chain G: W.68, K.136 Ligands: IOD.63 Ligand excluded by PLIP IOD.66: 4 residues within 4Å: Chain G: G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.67: 1 residues within 4Å: Chain G: A.88 Ligand excluded by PLIP IOD.72: 3 residues within 4Å: Chain H: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.73: 4 residues within 4Å: Chain H: G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.74: 1 residues within 4Å: Chain H: A.88 Ligand excluded by PLIP IOD.75: 3 residues within 4Å: Chain H: A.79, S.81, R.291 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: N.357, G.358, I.359, R.360, I.366, D.367, L.368, P.369 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.357, A:R.360, A:R.360, A:D.367, A:D.367 Water bridges: A:R.360 GOL.30: 8 residues within 4Å: Chain C: N.357, G.358, I.359, R.360, I.366, D.367, L.368, P.369 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.357, C:R.360, C:R.360, C:D.367, C:D.367 Water bridges: C:R.360 GOL.49: 8 residues within 4Å: Chain E: N.357, G.358, I.359, R.360, I.366, D.367, L.368, P.369 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.357, E:R.360, E:R.360, E:D.367, E:D.367 Water bridges: E:R.360 GOL.68: 8 residues within 4Å: Chain G: N.357, G.358, I.359, R.360, I.366, D.367, L.368, P.369 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:N.357, G:R.360, G:R.360, G:D.367, G:D.367 Water bridges: G:R.360

8 x PBE: 1,1-DIMETHYL-PROLINIUM(Non-covalent)

PBE.12: 15 residues within 4Å: Chain A: I.44, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.315, A.317, W.343 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.44, A:Y.78 Hydrogen bonds: A:Y.157, A:Q.184, A:D.216, A:N.218 Water bridges: A:Y.157 Salt bridges: A:K.186, A:K.288 pi-Cation interactions: A:W.343, A:W.343 PBE.19: 14 residues within 4Å: Chain B: Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.13 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.78 Hydrogen bonds: B:Y.78, B:Y.78, B:Y.157, B:Q.184, B:N.218 Water bridges: B:E.241, B:D.315, B:D.315 Salt bridges: B:K.186, B:K.288 pi-Cation interactions: B:W.343, B:W.343 PBE.31: 15 residues within 4Å: Chain C: I.44, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.315, A.317, W.343 Ligands: MG.20 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.44, C:Y.78 Hydrogen bonds: C:Y.157, C:Q.184, C:D.216, C:N.218 Water bridges: C:Y.157 Salt bridges: C:K.186, C:K.288 pi-Cation interactions: C:W.343, C:W.343 PBE.38: 14 residues within 4Å: Chain D: Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.32 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:Y.78 Hydrogen bonds: D:Y.78, D:Y.78, D:Y.157, D:Q.184, D:N.218 Water bridges: D:E.241, D:D.315, D:D.315 Salt bridges: D:K.186, D:K.288 pi-Cation interactions: D:W.343, D:W.343 PBE.50: 15 residues within 4Å: Chain E: I.44, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.315, A.317, W.343 Ligands: MG.39 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:I.44, E:Y.78 Hydrogen bonds: E:Y.157, E:Q.184, E:D.216, E:N.218 Water bridges: E:Y.157 Salt bridges: E:K.186, E:K.288 pi-Cation interactions: E:W.343, E:W.343 PBE.57: 14 residues within 4Å: Chain F: Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.51 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:Y.78 Hydrogen bonds: F:Y.78, F:Y.78, F:Y.157, F:Q.184, F:N.218 Water bridges: F:E.241, F:D.315, F:D.315 Salt bridges: F:K.186, F:K.288 pi-Cation interactions: F:W.343, F:W.343 PBE.69: 15 residues within 4Å: Chain G: I.44, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.315, A.317, W.343 Ligands: MG.58 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:I.44, G:Y.78 Hydrogen bonds: G:Y.157, G:Q.184, G:D.216, G:N.218 Water bridges: G:Y.157 Salt bridges: G:K.186, G:K.288 pi-Cation interactions: G:W.343, G:W.343 PBE.76: 14 residues within 4Å: Chain H: Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.70 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:Y.78 Hydrogen bonds: H:Y.78, H:Y.78, H:Y.157, H:Q.184, H:N.218 Water bridges: H:E.241, H:D.315, H:D.315 Salt bridges: H:K.186, H:K.288 pi-Cation interactions: H:W.343, H:W.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, R. et al., Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio (2014)

Release Date

2013-03-06

Peptides

Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein: 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/muconate lactonizing enzyme, N-terminal domain protein

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