SMTL ID : 4gme.1

Crystal structure of mannonate dehydratase (target EFI-502209) from caulobacter crescentus cb15 complexed with magnesium and d-mannonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.234, E.260, E.286, R.307 Ligands: CO3.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.234, A:E.260, A:E.286, H2O.1 MG.5: 6 residues within 4Å: Chain B: D.234, E.260, D.261, E.286, R.307 Ligands: CS2.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.234, B:E.260, B:E.286, H2O.11 MG.8: 5 residues within 4Å: Chain C: D.234, E.260, E.286, R.307 Ligands: CO3.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.234, C:E.260, C:E.286, H2O.20 MG.12: 6 residues within 4Å: Chain D: D.234, E.260, D.261, E.286, R.307 Ligands: CS2.14 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.234, D:E.260, D:E.286, H2O.30 MG.15: 5 residues within 4Å: Chain E: D.234, E.260, E.286, R.307 Ligands: CO3.18 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.234, E:E.260, E:E.286, H2O.40 MG.19: 6 residues within 4Å: Chain F: D.234, E.260, D.261, E.286, R.307 Ligands: CS2.21 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.234, F:E.260, F:E.286, H2O.50 MG.22: 5 residues within 4Å: Chain G: D.234, E.260, E.286, R.307 Ligands: CO3.25 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.234, G:E.260, G:E.286, H2O.59 MG.26: 6 residues within 4Å: Chain H: D.234, E.260, D.261, E.286, R.307 Ligands: CS2.28 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.234, H:E.260, H:E.286, H2O.69

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 8 residues within 4Å: Chain A: G.102, G.103, P.104, V.105, A.106 Chain B: P.104, V.105 Ligands: CL.6 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain A: P.104, V.105 Chain B: G.102, G.103, V.105, A.106 Ligands: CL.2 Ligand excluded by PLIP CL.9: 8 residues within 4Å: Chain C: G.102, G.103, P.104, V.105, A.106 Chain D: P.104, V.105 Ligands: CL.13 Ligand excluded by PLIP CL.13: 7 residues within 4Å: Chain C: P.104, V.105 Chain D: G.102, G.103, V.105, A.106 Ligands: CL.9 Ligand excluded by PLIP CL.16: 8 residues within 4Å: Chain E: G.102, G.103, P.104, V.105, A.106 Chain F: P.104, V.105 Ligands: CL.20 Ligand excluded by PLIP CL.20: 7 residues within 4Å: Chain E: P.104, V.105 Chain F: G.102, G.103, V.105, A.106 Ligands: CL.16 Ligand excluded by PLIP CL.23: 8 residues within 4Å: Chain G: G.102, G.103, P.104, V.105, A.106 Chain H: P.104, V.105 Ligands: CL.27 Ligand excluded by PLIP CL.27: 7 residues within 4Å: Chain G: P.104, V.105 Chain H: G.102, G.103, V.105, A.106 Ligands: CL.23 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: N.61, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Chain B: Y.99, W.100 Ligands: CO3.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.61, A:H.236, A:D.340 Water bridges: A:Y.183, A:T.339 GOL.10: 11 residues within 4Å: Chain C: N.61, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Chain D: Y.99, W.100 Ligands: CO3.11 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.61, C:H.236, C:D.340 Water bridges: C:Y.183, C:T.339 GOL.17: 11 residues within 4Å: Chain E: N.61, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Chain F: Y.99, W.100 Ligands: CO3.18 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.61, E:H.236, E:D.340 Water bridges: E:Y.183, E:T.339 GOL.24: 11 residues within 4Å: Chain G: N.61, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Chain H: Y.99, W.100 Ligands: CO3.25 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:N.61, G:H.236, G:D.340 Water bridges: G:Y.183, G:T.339

4 x CO3: CARBONATE ION(Non-functional Binders)

CO3.4: 13 residues within 4Å: Chain A: R.171, Y.183, D.234, H.236, E.260, E.286, R.307, H.336, A.338, E.363, M.365 Ligands: MG.1, GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.171, A:Y.183, A:E.286 CO3.11: 13 residues within 4Å: Chain C: R.171, Y.183, D.234, H.236, E.260, E.286, R.307, H.336, A.338, E.363, M.365 Ligands: MG.8, GOL.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.171, C:Y.183, C:E.286 CO3.18: 13 residues within 4Å: Chain E: R.171, Y.183, D.234, H.236, E.260, E.286, R.307, H.336, A.338, E.363, M.365 Ligands: MG.15, GOL.17 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.171, E:Y.183, E:H.236, E:E.363 CO3.25: 13 residues within 4Å: Chain G: R.171, Y.183, D.234, H.236, E.260, E.286, R.307, H.336, A.338, E.363, M.365 Ligands: MG.22, GOL.24 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.171, G:Y.183, G:E.286

4 x CS2: D-MANNONIC ACID(Non-covalent)

CS2.7: 18 residues within 4Å: Chain A: Y.99, W.100 Chain B: N.61, R.171, Y.183, D.234, H.236, E.260, E.286, R.307, H.336, A.338, D.340, E.363, M.365, L.413, W.426 Ligands: MG.5 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.61, B:H.236, B:H.236 Water bridges: B:Y.144, B:R.171, B:D.340, A:Y.99, A:Y.99 Salt bridges: B:R.171, B:R.307, B:H.336 CS2.14: 18 residues within 4Å: Chain C: Y.99, W.100 Chain D: N.61, R.171, Y.183, D.234, H.236, E.260, E.286, R.307, H.336, A.338, D.340, E.363, M.365, L.413, W.426 Ligands: MG.12 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.61, D:H.236, D:H.236 Water bridges: D:Y.144, D:R.171, D:D.340, C:Y.99, C:Y.99 Salt bridges: D:R.171, D:R.307, D:H.336 CS2.21: 18 residues within 4Å: Chain E: Y.99, W.100 Chain F: N.61, R.171, Y.183, D.234, H.236, E.260, E.286, R.307, H.336, A.338, D.340, E.363, M.365, L.413, W.426 Ligands: MG.19 11 PLIP interactions: 9 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:N.61, F:H.236, F:H.236 Water bridges: F:Y.144, F:R.171, F:D.340, E:Y.99, E:Y.99 Salt bridges: F:R.171, F:R.307, F:H.336 CS2.28: 18 residues within 4Å: Chain G: Y.99, W.100 Chain H: N.61, R.171, Y.183, D.234, H.236, E.260, E.286, R.307, H.336, A.338, D.340, E.363, M.365, L.413, W.426 Ligands: MG.26 11 PLIP interactions: 9 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:N.61, H:H.236, H:H.236 Water bridges: H:Y.144, H:R.171, H:D.340, G:Y.99, G:Y.99 Salt bridges: H:R.171, H:R.307, H:H.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal Structure of Mannonate Dehydratase from Caulobacter Crescentus Cb15. To be Published

Release Date

2012-09-12

Peptides

Mandelate racemase/muconate lactonizing enzyme family: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

E
A

F
C

G
A

H
C

Mandelate racemase/muconate lactonizing enzyme family