SMTL ID : 3r25.7 (6 other biounits)

Crystal structure of enolase superfamily member from Vibrionales bacterium complexed with Mg and Glycerol in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-octamer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.207, E.233, E.259, R.280 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.207, A:E.233, A:E.259, H2O.1, H2O.1, H2O.1 MG.3: 3 residues within 4Å: Chain B: D.207, E.233, E.259 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.207, B:E.233, B:E.259, H2O.9, H2O.9, H2O.18 MG.4: 1 residues within 4Å: Chain B: K.346 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: D.207, E.233, E.259 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.207, C:E.233, C:E.259, H2O.19, H2O.19, H2O.19 MG.8: 4 residues within 4Å: Chain D: D.207, E.233, E.259, R.280 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.207, D:E.233, D:E.259, H2O.27, H2O.27, H2O.27 MG.9: 1 residues within 4Å: Chain D: K.346 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain E: R.153, D.207, E.233, E.259, R.280 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.207, E:E.233, E:E.259, H2O.37, H2O.37, H2O.37 MG.13: 4 residues within 4Å: Chain F: D.207, E.233, E.259, R.280 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.207, F:E.233, F:E.259, H2O.45, H2O.45, H2O.45 MG.15: 3 residues within 4Å: Chain G: D.207, E.233, E.259 6 PLIP interactions: 3 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.207, G:E.233, G:E.259, H2O.53, H2O.54, H2O.62 MG.17: 4 residues within 4Å: Chain H: D.207, E.233, E.259, R.280 6 PLIP interactions: 3 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.207, H:E.233, H:E.259, H2O.62, H2O.62, H2O.62

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: Q.43, Q.44, H.209, E.259, H.309, P.311, D.313, W.388 Chain B: Y.81, W.82 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.43, A:Q.44, A:H.209, A:H.309 Water bridges: B:Y.81 GOL.5: 10 residues within 4Å: Chain A: Y.81, W.82 Chain B: Q.43, Q.44, H.209, E.259, H.309, P.311, D.313, W.388 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.43, B:Q.44, B:H.209, B:H.309 GOL.7: 9 residues within 4Å: Chain C: Q.43, Q.44, H.209, E.259, H.309, P.311, D.313 Chain D: Y.81, W.82 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.43, C:Q.44, C:H.209, C:H.309 GOL.10: 10 residues within 4Å: Chain C: Y.81, W.82 Chain D: Q.43, Q.44, H.209, E.259, H.309, P.311, D.313, W.388 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.43, D:Q.44, D:H.209, D:H.309 GOL.12: 11 residues within 4Å: Chain E: Q.43, Q.44, Y.159, H.209, E.259, H.309, P.311, D.313, W.388 Chain F: Y.81, W.82 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.43, E:Q.44, E:H.209, E:H.309 Water bridges: E:D.313 GOL.14: 10 residues within 4Å: Chain E: Y.81, W.82 Chain F: Q.43, Q.44, H.209, E.259, H.309, P.311, D.313, W.388 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.43, F:Q.44, F:H.209, F:H.309 GOL.16: 10 residues within 4Å: Chain G: Q.43, Q.44, H.209, E.259, H.309, P.311, D.313, W.388 Chain H: Y.81, W.82 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Q.43, G:Q.44, G:H.209, G:H.309 GOL.18: 10 residues within 4Å: Chain G: Y.81, W.82 Chain H: Q.43, Q.44, H.209, E.259, H.309, P.311, D.313, W.388 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:Q.43, H:Q.44, H:H.209, H:H.309 Water bridges: G:Y.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of enolase superfamily member from VIBRIONALES BACTERIUM complexed with Mg and Glycerol in the active site. To be Published

Release Date

2012-03-14

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

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