SMTL ID : 3rgt.3 (2 other biounits)

Crystal structure of d-mannonate dehydratase from Chromohalobacter salexigens complexed with D-Arabinohydroxamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

8 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: D.213, E.239, E.265, R.286 Ligands: EZ4.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:E.239, A:E.265, H2O.8 CO.3: 6 residues within 4Å: Chain B: D.213, H.215, E.239, E.265, R.286 Ligands: EZ4.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:E.239, B:E.265, H2O.16 CO.5: 6 residues within 4Å: Chain C: D.213, H.215, E.239, E.265, R.286 Ligands: EZ4.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.213, C:E.239, C:E.265, H2O.25 CO.7: 5 residues within 4Å: Chain D: D.213, E.239, E.265, R.286 Ligands: EZ4.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.213, D:E.239, D:E.265, H2O.33 CO.9: 5 residues within 4Å: Chain E: D.213, E.239, E.265, R.286 Ligands: EZ4.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.213, E:E.239, E:E.265, H2O.41 CO.11: 6 residues within 4Å: Chain F: D.213, H.215, E.239, E.265, R.286 Ligands: EZ4.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.213, F:E.239, F:E.265, H2O.49 CO.13: 6 residues within 4Å: Chain G: D.213, H.215, E.239, E.265, R.286 Ligands: EZ4.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.213, G:E.239, G:E.265, H2O.58 CO.15: 5 residues within 4Å: Chain H: D.213, E.239, E.265, R.286 Ligands: EZ4.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.213, H:E.239, H:E.265, H2O.66

8 x EZ4: (2S,3R,4R)-2,3,4,5-tetrahydroxy-N-oxo-pentanamide(Non-covalent)

EZ4.2: 15 residues within 4Å: Chain A: N.39, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, W.405 Chain C: Y.77, W.78 Ligands: CO.1 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.39, A:R.149, A:H.215, A:R.286, C:Y.77 Water bridges: A:T.318 EZ4.4: 18 residues within 4Å: Chain B: N.39, R.149, Y.161, P.173, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Chain D: Y.77, W.78 Ligands: CO.3 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.39, B:R.149, B:Y.161, B:Y.161, B:H.215, B:R.286 Water bridges: B:Y.122, B:Y.122, D:Y.77 EZ4.6: 16 residues within 4Å: Chain A: Y.77, W.78 Chain C: N.39, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Ligands: CO.5 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Water bridges: A:Y.77, C:Y.122, C:Y.122 Hydrogen bonds: C:N.39, C:R.149, C:H.215, C:R.286 EZ4.8: 15 residues within 4Å: Chain B: Y.77, W.78 Chain D: N.39, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, W.405 Ligands: CO.7 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.39, D:R.149, D:H.215, D:R.286, B:Y.77 Water bridges: D:T.318 EZ4.10: 15 residues within 4Å: Chain E: N.39, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, W.405 Chain G: Y.77, W.78 Ligands: CO.9 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain G Hydrogen bonds: E:N.39, E:R.149, E:H.215, E:R.286, G:Y.77 Water bridges: E:T.318 EZ4.12: 18 residues within 4Å: Chain F: N.39, R.149, Y.161, P.173, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Chain H: Y.77, W.78 Ligands: CO.11 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain H Hydrogen bonds: F:N.39, F:R.149, F:Y.161, F:Y.161, F:H.215, F:R.286 Water bridges: F:Y.122, F:Y.122, H:Y.77 EZ4.14: 16 residues within 4Å: Chain E: Y.77, W.78 Chain G: N.39, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, L.392, W.405 Ligands: CO.13 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:N.39, G:R.149, G:H.215, G:R.286 Water bridges: G:Y.122, G:Y.122, E:Y.77 EZ4.16: 15 residues within 4Å: Chain F: Y.77, W.78 Chain H: N.39, R.149, D.213, H.215, E.239, E.265, R.286, H.315, P.317, D.319, E.342, W.405 Ligands: CO.15 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain F Hydrogen bonds: H:N.39, H:R.149, H:D.213, H:H.215, H:R.286, F:Y.77 Water bridges: H:T.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of d-mannonate dehydratase from Chromohalobacter salexigens complexed with d-arabinohydroxamate. To be Published

Release Date

2012-04-11

Peptides

D-mannonate dehydratase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

D-mannonate dehydratase

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