SMTL ID : 2pmq.1

Crystal structure of a mandelate racemase/muconate lactonizing enzyme from Roseovarius sp. HTCC2601

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-octamer

Ligands

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

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.2: 6 residues within 4Å: Chain A: Y.58, Q.163, D.195, N.197, E.220, D.243 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.195, A:E.220, A:D.243, H2O.1, H2O.3, H2O.13 MG.3: 7 residues within 4Å: Chain A: H.237 Chain C: H.237 Chain E: H.237 Chain G: H.237 Ligands: MG.8, MG.13, MG.18 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: A:H.237, C:H.237, E:H.237, G:H.237, H2O.2, H2O.9 MG.4: 4 residues within 4Å: Chain B: Q.163, D.195, E.220, D.243 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.195, B:E.220, B:D.243, H2O.15, H2O.16, H2O.18 MG.5: 7 residues within 4Å: Chain B: H.237 Chain D: H.237 Chain F: H.237 Chain H: H.237 Ligands: MG.10, MG.15, MG.20 6 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: F:H.237, D:H.237, H2O.17, H2O.43, H2O.70, H2O.96 MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain C: Y.58, Q.163, D.195, N.197, E.220, D.243 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.195, C:E.220, C:D.243, H2O.27, H2O.29, H2O.40 MG.8: 7 residues within 4Å: Chain A: H.237 Chain C: H.237 Chain E: H.237 Chain G: H.237 Ligands: MG.3, MG.13, MG.18 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: A:H.237, C:H.237, E:H.237, G:H.237, H2O.29, H2O.35 MG.9: 4 residues within 4Å: Chain D: Q.163, D.195, E.220, D.243 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.195, D:E.220, D:D.243, H2O.42, H2O.42, H2O.45 MG.10: 7 residues within 4Å: Chain B: H.237 Chain D: H.237 Chain F: H.237 Chain H: H.237 Ligands: MG.5, MG.15, MG.20 6 PLIP interactions: 1 interactions with chain H, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: H:H.237, B:H.237, H2O.17, H2O.43, H2O.70, H2O.96 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 6 residues within 4Å: Chain E: Y.58, Q.163, D.195, N.197, E.220, D.243 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.195, E:E.220, E:D.243, H2O.54, H2O.56, H2O.66 MG.13: 7 residues within 4Å: Chain A: H.237 Chain C: H.237 Chain E: H.237 Chain G: H.237 Ligands: MG.3, MG.8, MG.18 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: A:H.237, C:H.237, E:H.237, G:H.237, H2O.55, H2O.62 MG.14: 4 residues within 4Å: Chain F: Q.163, D.195, E.220, D.243 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.195, F:E.220, F:D.243, H2O.68, H2O.68, H2O.71 MG.15: 7 residues within 4Å: Chain B: H.237 Chain D: H.237 Chain F: H.237 Chain H: H.237 Ligands: MG.5, MG.10, MG.20 6 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: H:H.237, D:H.237, H2O.17, H2O.43, H2O.70, H2O.96 MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 6 residues within 4Å: Chain G: Y.58, Q.163, D.195, N.197, E.220, D.243 6 PLIP interactions: 3 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.195, G:E.220, G:D.243, H2O.80, H2O.82, H2O.93 MG.18: 7 residues within 4Å: Chain A: H.237 Chain C: H.237 Chain E: H.237 Chain G: H.237 Ligands: MG.3, MG.8, MG.13 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain G, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: C:H.237, A:H.237, G:H.237, E:H.237, H2O.81, H2O.88 MG.19: 4 residues within 4Å: Chain H: Q.163, D.195, E.220, D.243 6 PLIP interactions: 3 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.195, H:E.220, H:D.243, H2O.94, H2O.95, H2O.98 MG.20: 7 residues within 4Å: Chain B: H.237 Chain D: H.237 Chain F: H.237 Chain H: H.237 Ligands: MG.5, MG.10, MG.15 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: B:H.237, F:H.237, H2O.17, H2O.43, H2O.70, H2O.96

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

2007-05-08

Peptides

Mandelate racemase/muconate lactonizing enzyme: 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