SMTL ID : 4ihc.1

Crystal structure of probable mannonate dehydratase Dd703_0947 (target EFI-502222) from Dickeya dadantii Ech703

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: 4 residues within 4Å: Chain A: D.246, E.272, E.298 Ligands: FMT.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.246, A:E.272, A:E.298, H2O.4, H2O.5 MG.7: 5 residues within 4Å: Chain B: D.246, E.272, E.298, R.319 Ligands: FMT.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.246, B:E.272, B:E.298, H2O.14, H2O.15 MG.15: 7 residues within 4Å: Chain C: D.246, H.248, E.272, D.273, E.298, R.319 Ligands: FMT.17 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.246, C:E.272, C:E.298, H2O.24, H2O.27 MG.23: 6 residues within 4Å: Chain D: D.246, E.272, D.273, E.298, R.319 Ligands: FMT.28 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.246, D:E.272, D:E.298, H2O.34, H2O.37 MG.31: 5 residues within 4Å: Chain E: D.246, E.272, E.298, R.319 Ligands: FMT.35 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.246, E:E.272, E:E.298, H2O.43, H2O.43 MG.39: 4 residues within 4Å: Chain F: D.246, E.272, E.298 Ligands: FMT.41 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.246, F:E.272, F:E.298, H2O.52, H2O.56 MG.48: 4 residues within 4Å: Chain G: D.246, E.272, E.298 Ligands: FMT.52 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.246, G:E.272, G:E.298, H2O.60, H2O.66 MG.53: 4 residues within 4Å: Chain H: D.246, E.272, E.298 Ligands: FMT.57 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.246, H:E.272, H:E.298, H2O.68, H2O.71

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: Q.66, H.248, H.348, P.350, D.352, W.427 Chain B: Y.103, W.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.66, A:H.248, A:D.352 GOL.5: 6 residues within 4Å: Chain A: E.50, T.51, P.54, G.55, L.56, Y.57 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.50, A:T.51, A:T.51, A:G.55 GOL.8: 10 residues within 4Å: Chain A: Y.103, W.104 Chain B: Q.66, H.248, E.298, H.348, P.350, D.352, W.427 Ligands: FMT.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.66, B:H.248, B:D.352 GOL.10: 7 residues within 4Å: Chain A: E.278, R.439 Chain B: W.95, A.99, V.100, R.105, N.106 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.106, A:R.439, A:R.439 Water bridges: B:N.106, B:N.106 GOL.16: 10 residues within 4Å: Chain C: Q.66, H.248, E.298, H.348, P.350, D.352, W.427 Chain G: Y.103, W.104 Ligands: FMT.17 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.66, C:H.248, C:D.352 Water bridges: C:D.352 GOL.21: 7 residues within 4Å: Chain C: E.278, R.439 Chain G: Q.96, A.99, V.100, R.105, N.106 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain C Hydrogen bonds: G:N.106, C:E.278, C:R.439, C:R.439 Water bridges: G:A.99, G:N.111 GOL.24: 9 residues within 4Å: Chain D: Q.66, H.248, E.298, H.348, P.350, D.352, W.427 Chain H: Y.103 Ligands: FMT.28 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.66, D:H.248, D:D.352 GOL.25: 7 residues within 4Å: Chain D: E.50, T.51, E.53, P.54, G.55, L.56, Y.57 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.51, D:G.55 GOL.32: 9 residues within 4Å: Chain E: Q.66, H.248, E.298, H.348, P.350, D.352, W.427 Chain F: Y.103, W.104 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.66, E:H.248, E:E.298, E:D.352 GOL.40: 10 residues within 4Å: Chain E: Y.103, W.104 Chain F: Q.66, H.248, E.298, H.348, P.350, D.352, W.427 Ligands: FMT.41 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.66, F:H.248, F:D.352 Water bridges: F:G.351 GOL.46: 6 residues within 4Å: Chain F: E.50, T.51, E.53, G.55, L.56, Y.57 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.51, F:T.51, F:G.55 GOL.49: 10 residues within 4Å: Chain C: Y.103, W.104 Chain G: Q.66, H.248, E.298, H.348, P.350, D.352, W.427 Ligands: FMT.52 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:Q.66, G:H.248, G:D.352 Water bridges: G:G.351, G:D.352, G:W.427, C:Y.103 GOL.54: 9 residues within 4Å: Chain D: Y.103, W.104 Chain H: Q.66, H.248, E.298, H.348, P.350, D.352, W.427 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Q.66, H:H.248, H:D.352 Water bridges: H:G.351 GOL.56: 6 residues within 4Å: Chain D: Q.96, V.100, R.105, N.106 Chain H: E.278, R.439 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain D Hydrogen bonds: H:E.278, H:R.439, D:N.106 Water bridges: D:N.106

9 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 8 residues within 4Å: Chain A: R.175, D.246, E.272, E.298, R.319, H.348, E.375 Ligands: MG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.175, A:D.246, A:R.319, A:H.348 FMT.11: 8 residues within 4Å: Chain B: D.246, E.272, E.298, R.319, H.348, E.375 Ligands: MG.7, GOL.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.319, B:H.348 Water bridges: B:Y.148 FMT.17: 9 residues within 4Å: Chain C: R.175, D.246, E.272, E.298, R.319, H.348, E.375 Ligands: MG.15, GOL.16 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.175, C:R.319, C:E.375 FMT.28: 10 residues within 4Å: Chain D: H.150, R.175, D.246, E.272, E.298, R.319, H.348, E.375 Ligands: MG.23, GOL.24 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.175, D:D.246, D:R.319, D:H.348 FMT.35: 8 residues within 4Å: Chain E: R.175, D.246, E.272, E.298, R.319, H.348, E.375 Ligands: MG.31 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.175, E:E.272, E:R.319 Water bridges: E:Y.148 FMT.41: 10 residues within 4Å: Chain F: H.150, R.175, D.246, E.272, E.298, R.319, H.348, E.375 Ligands: MG.39, GOL.40 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.175, F:D.246, F:R.319 Water bridges: F:D.246 FMT.44: 4 residues within 4Å: Chain E: V.100, R.105 Chain F: E.278, R.439 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Water bridges: E:N.106 Hydrogen bonds: F:R.439 FMT.52: 9 residues within 4Å: Chain G: R.175, D.246, E.272, E.298, R.319, H.348, E.375 Ligands: MG.48, GOL.49 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:R.175, G:D.246, G:E.272, G:R.319 FMT.57: 8 residues within 4Å: Chain H: R.175, D.246, E.272, E.298, R.319, H.348, E.375 Ligands: MG.53 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:R.175, H:R.319, H:H.348

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

IOD.4: 3 residues within 4Å: Chain A: G.139, K.140 Chain C: T.89 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: P.219, V.251, T.252, T.255 Ligand excluded by PLIP IOD.12: 8 residues within 4Å: Chain A: G.107, P.108, I.109, M.110 Chain B: G.107, P.108, I.109, M.110 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain B: T.89 Chain D: G.139, K.140 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain B: P.219, V.251, T.252, T.255 Ligand excluded by PLIP IOD.19: 8 residues within 4Å: Chain C: G.107, P.108, I.109, M.110 Chain G: G.107, P.108, I.109, M.110 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain A: T.89 Chain C: G.139, K.140 Ligand excluded by PLIP IOD.22: 4 residues within 4Å: Chain C: P.219, V.251, T.252, T.255 Ligand excluded by PLIP IOD.27: 8 residues within 4Å: Chain D: G.107, P.108, I.109, M.110 Chain H: G.107, P.108, I.109, M.110 Ligand excluded by PLIP IOD.29: 3 residues within 4Å: Chain B: G.139, K.140 Chain D: T.89 Ligand excluded by PLIP IOD.30: 4 residues within 4Å: Chain D: P.219, V.251, T.252, T.255 Ligand excluded by PLIP IOD.36: 3 residues within 4Å: Chain E: G.139, K.140 Chain G: T.89 Ligand excluded by PLIP IOD.37: 3 residues within 4Å: Chain E: T.89 Chain G: G.139, K.140 Ligand excluded by PLIP IOD.38: 5 residues within 4Å: Chain E: P.219, E.220, V.251, T.252, T.255 Ligand excluded by PLIP IOD.43: 8 residues within 4Å: Chain E: G.107, P.108, I.109, M.110 Chain F: G.107, P.108, I.109, M.110 Ligand excluded by PLIP IOD.45: 3 residues within 4Å: Chain F: T.89 Chain H: G.139, K.140 Ligand excluded by PLIP IOD.47: 4 residues within 4Å: Chain F: P.219, V.251, T.252, T.255 Ligand excluded by PLIP IOD.58: 3 residues within 4Å: Chain F: G.139, K.140 Chain H: T.89 Ligand excluded by PLIP IOD.59: 4 residues within 4Å: Chain H: P.219, V.251, T.252, T.255 Ligand excluded by PLIP

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

CL.9: 3 residues within 4Å: Chain A: A.74, A.113 Chain B: R.67 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain C: R.67 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain D: R.67 Chain H: A.74, M.110, A.113 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain E: R.67 Chain F: A.74 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain E: K.86, D.87 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain E: A.74, M.79, M.110 Chain F: R.67 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain G: P.219, V.251, T.252, T.255 Ligand excluded by PLIP CL.51: 3 residues within 4Å: Chain C: A.74, M.79 Chain G: R.67 Ligand excluded by PLIP CL.55: 2 residues within 4Å: Chain D: A.113 Chain H: R.67 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal structure of mannonate dehydratase Dd703_0947 from Dickeya dadantii Ech703. To be Published

Release Date

2013-01-16

Peptides

Mandelate racemase/muconate lactonizing protein: 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 protein