SMTL ID : 4h2h.1

Crystal structure of an enolase (mandalate racemase subgroup, target EFI-502101) from Pelagibaca bermudensis htcc2601, with bound mg and l-4-hydroxyproline betaine (betonicine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: Q.170, D.202, E.227, D.250 Ligands: 0XW.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.202, A:E.227, A:D.250, H2O.2 MG.12: 6 residues within 4Å: Chain B: Q.170, D.202, N.204, E.227, D.250 Ligands: 0XW.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.202, B:E.227, B:D.250, H2O.13 MG.21: 6 residues within 4Å: Chain C: Q.170, D.202, N.204, E.227, D.250 Ligands: 0XW.22 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.202, C:E.227, C:D.250, H2O.23 MG.34: 7 residues within 4Å: Chain D: Y.65, Q.170, D.202, N.204, E.227, D.250 Ligands: 0XW.35 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.202, D:E.227, D:D.250, H2O.34 MG.45: 5 residues within 4Å: Chain E: Q.170, D.202, E.227, D.250 Ligands: 0XW.46 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.202, E:E.227, E:D.250, H2O.52 MG.55: 6 residues within 4Å: Chain F: Q.170, K.172, D.202, E.227, D.250 Ligands: 0XW.56 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.202, F:E.227, F:D.250, H2O.55 MG.65: 8 residues within 4Å: Chain G: Y.65, Q.170, K.172, D.202, N.204, E.227, D.250 Ligands: 0XW.66 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.202, G:E.227, G:D.250, H2O.63 MG.75: 7 residues within 4Å: Chain H: Q.170, K.172, D.202, N.204, E.227, D.250 Ligands: 0XW.76 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.202, H:E.227, H:D.250, H2O.72

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 4 residues within 4Å: Chain A: H.244 Chain C: H.244 Chain E: H.244 Chain H: H.244 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain H, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.244, E:H.244, H:H.244, A:H.244, H2O.23, H2O.23 NI.13: 4 residues within 4Å: Chain B: H.244 Chain D: H.244 Chain F: H.244 Chain G: H.244 6 PLIP interactions: 1 interactions with chain G, 1 interactions with chain B, 1 interactions with chain F, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: G:H.244, B:H.244, F:H.244, D:H.244, H2O.34, H2O.52

8 x 0XW: (2S,4R)-4-hydroxy-1,1-dimethylpyrrolidinium-2-carboxylate(Non-covalent)

0XW.3: 16 residues within 4Å: Chain A: Y.29, V.61, Y.65, Y.143, S.145, Q.170, K.172, D.202, N.204, E.227, D.250, K.274, D.302, A.303, W.329 Ligands: MG.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.65 Hydrogen bonds: A:Y.65, A:Q.170, A:N.204, A:A.303 Water bridges: A:K.274 Salt bridges: A:K.172, A:K.274 pi-Cation interactions: A:W.329, A:W.329 0XW.14: 17 residues within 4Å: Chain B: Y.29, V.61, Y.65, Y.143, S.145, Q.170, K.172, D.202, N.204, E.227, D.250, K.274, D.301, D.302, A.303, W.329 Ligands: MG.12 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.65 Hydrogen bonds: B:Y.65, B:Y.143, B:Y.143, B:Q.170, B:D.202, B:N.204, B:A.303 Water bridges: B:K.274 Salt bridges: B:K.172, B:K.274 pi-Cation interactions: B:W.329, B:W.329 0XW.22: 17 residues within 4Å: Chain C: Y.29, V.61, Y.65, Y.143, S.145, Q.170, K.172, D.202, N.204, E.227, D.250, K.274, D.301, D.302, A.303, W.329 Ligands: MG.21 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.65 Hydrogen bonds: C:Y.143, C:Q.170, C:N.204, C:A.303 Water bridges: C:D.301 Salt bridges: C:K.172, C:K.274 pi-Cation interactions: C:W.329, C:W.329 0XW.35: 16 residues within 4Å: Chain D: Y.29, V.61, Y.65, Y.143, S.145, Q.170, K.172, D.202, N.204, E.227, D.250, K.274, D.301, A.303, W.329 Ligands: MG.34 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.65 Hydrogen bonds: D:Y.65, D:Y.143, D:Y.143, D:Q.170, D:N.204, D:A.303 Water bridges: D:D.301 Salt bridges: D:K.172, D:K.274 pi-Cation interactions: D:W.329, D:W.329 0XW.46: 14 residues within 4Å: Chain E: V.61, Y.65, Y.143, S.145, Q.170, K.172, D.202, E.227, D.250, K.274, D.301, A.303, W.329 Ligands: MG.45 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:Y.65, E:Q.170, E:D.202, E:A.303 Water bridges: E:E.227 Salt bridges: E:K.172, E:K.274 pi-Cation interactions: E:W.329, E:W.329 0XW.56: 17 residues within 4Å: Chain F: Y.29, V.61, Y.65, Y.143, S.145, Q.170, K.172, D.202, N.204, E.227, D.250, K.274, D.301, D.302, A.303, W.329 Ligands: MG.55 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:Y.65 Hydrogen bonds: F:Y.65, F:Y.143, F:Q.170, F:D.202, F:N.204, F:A.303 Salt bridges: F:K.172, F:K.274 pi-Cation interactions: F:W.329, F:W.329 0XW.66: 17 residues within 4Å: Chain G: Y.29, V.61, Y.65, Y.143, S.145, Q.170, K.172, D.202, N.204, E.227, D.250, K.274, D.301, D.302, A.303, W.329 Ligands: MG.65 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:Y.65 Hydrogen bonds: G:Y.65, G:Y.65, G:Q.170, G:N.204, G:A.303 Water bridges: G:D.301 Salt bridges: G:K.172, G:K.274 pi-Cation interactions: G:W.329, G:W.329 0XW.76: 17 residues within 4Å: Chain H: Y.29, V.61, Y.65, Y.143, S.145, Q.170, K.172, D.202, N.204, E.227, D.250, K.274, D.301, D.302, A.303, W.329 Ligands: MG.75 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:Y.65 Hydrogen bonds: H:Y.143, H:Y.143, H:Q.170, H:D.202, H:N.204, H:A.303 Water bridges: H:D.250 Salt bridges: H:K.172, H:K.274 pi-Cation interactions: H:W.329, H:W.329

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

IOD.4: 3 residues within 4Å: Chain A: G.194, G.196 Chain C: E.179 Ligand excluded by PLIP IOD.5: 4 residues within 4Å: Chain A: S.255, L.256, N.257 Chain D: A.293 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: P.322, R.323 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: R.277 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: R.97 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: K.45, I.47, P.366 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: H.338 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: E.342 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain B: G.194, G.196 Chain F: E.179 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain B: P.322, R.323 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain B: E.342 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain B: R.97 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain B: R.277 Ligand excluded by PLIP IOD.20: 1 residues within 4Å: Chain B: H.338 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain C: E.150, R.176 Ligand excluded by PLIP IOD.25: 1 residues within 4Å: Chain C: R.277 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain C: P.322, R.323 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain C: R.156, R.163 Ligand excluded by PLIP IOD.28: 1 residues within 4Å: Chain C: E.183 Ligand excluded by PLIP IOD.29: 1 residues within 4Å: Chain C: E.342 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain C: G.194, T.195, G.196 Ligand excluded by PLIP IOD.31: 1 residues within 4Å: Chain C: R.97 Ligand excluded by PLIP IOD.32: 2 residues within 4Å: Chain C: M.149, E.150 Ligand excluded by PLIP IOD.33: 1 residues within 4Å: Chain C: H.338 Ligand excluded by PLIP IOD.37: 1 residues within 4Å: Chain D: R.176 Ligand excluded by PLIP IOD.38: 2 residues within 4Å: Chain D: G.194, G.196 Ligand excluded by PLIP IOD.39: 1 residues within 4Å: Chain D: R.277 Ligand excluded by PLIP IOD.40: 2 residues within 4Å: Chain D: P.322, R.323 Ligand excluded by PLIP IOD.41: 1 residues within 4Å: Chain D: R.97 Ligand excluded by PLIP IOD.42: 4 residues within 4Å: Chain D: P.28, Y.29, R.30, G.147 Ligand excluded by PLIP IOD.43: 3 residues within 4Å: Chain D: V.24, V.25, N.26 Ligand excluded by PLIP IOD.44: 3 residues within 4Å: Chain D: T.52, I.53, K.122 Ligand excluded by PLIP IOD.48: 1 residues within 4Å: Chain E: R.176 Ligand excluded by PLIP IOD.49: 2 residues within 4Å: Chain E: P.322, R.323 Ligand excluded by PLIP IOD.50: 2 residues within 4Å: Chain E: A.66, R.277 Ligand excluded by PLIP IOD.51: 1 residues within 4Å: Chain E: R.97 Ligand excluded by PLIP IOD.52: 2 residues within 4Å: Chain E: G.147, V.148 Ligand excluded by PLIP IOD.53: 3 residues within 4Å: Chain E: T.52, I.53, K.122 Ligand excluded by PLIP IOD.54: 2 residues within 4Å: Chain E: G.194, G.196 Ligand excluded by PLIP IOD.57: 1 residues within 4Å: Chain F: R.277 Ligand excluded by PLIP IOD.58: 1 residues within 4Å: Chain F: R.176 Ligand excluded by PLIP IOD.59: 1 residues within 4Å: Chain F: E.183 Ligand excluded by PLIP IOD.60: 3 residues within 4Å: Chain F: G.194, T.195, G.196 Ligand excluded by PLIP IOD.61: 2 residues within 4Å: Chain F: P.322, R.323 Ligand excluded by PLIP IOD.62: 1 residues within 4Å: Chain F: E.342 Ligand excluded by PLIP IOD.63: 2 residues within 4Å: Chain F: R.156, R.163 Ligand excluded by PLIP IOD.64: 2 residues within 4Å: Chain F: M.149, E.150 Ligand excluded by PLIP IOD.67: 2 residues within 4Å: Chain G: P.322, R.323 Ligand excluded by PLIP IOD.68: 1 residues within 4Å: Chain G: R.277 Ligand excluded by PLIP IOD.69: 1 residues within 4Å: Chain G: R.176 Ligand excluded by PLIP IOD.70: 1 residues within 4Å: Chain G: H.338 Ligand excluded by PLIP IOD.71: 3 residues within 4Å: Chain G: T.52, I.53, K.122 Ligand excluded by PLIP IOD.72: 1 residues within 4Å: Chain G: R.97 Ligand excluded by PLIP IOD.73: 4 residues within 4Å: Chain D: E.179 Chain G: G.194, T.195, G.196 Ligand excluded by PLIP IOD.74: 2 residues within 4Å: Chain G: M.149, E.150 Ligand excluded by PLIP IOD.77: 2 residues within 4Å: Chain H: P.322, R.323 Ligand excluded by PLIP IOD.78: 1 residues within 4Å: Chain H: R.277 Ligand excluded by PLIP IOD.79: 2 residues within 4Å: Chain H: E.150, R.176 Ligand excluded by PLIP IOD.80: 2 residues within 4Å: Chain H: M.149, E.150 Ligand excluded by PLIP IOD.81: 1 residues within 4Å: Chain H: R.97 Ligand excluded by PLIP IOD.82: 3 residues within 4Å: Chain H: G.194, T.195, G.196 Ligand excluded by PLIP

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.23: 5 residues within 4Å: Chain C: A.155, R.156, K.187, E.190, A.191 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.155, C:E.190, C:A.191 Hydrogen bonds: C:A.155 MPD.36: 4 residues within 4Å: Chain C: F.233, E.237 Chain D: F.233, E.237 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.233, C:F.233 Hydrogen bonds: D:E.237 MPD.47: 5 residues within 4Å: Chain E: F.233, E.237 Chain F: F.233, E.237, T.258 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:F.233, F:F.233, F:F.233, E:F.233 Hydrogen bonds: E:E.237 Water bridges: E:E.234, E:E.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, S. et al., Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature (2013)

Release Date

2012-10-10

Peptides

Mandelate racemase/muconate lactonizing enzyme: 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/muconate lactonizing enzyme