SMTL ID : 4f4r.1 (1 other biounit)

Crystal structure of D-mannonate dehydratase homolog from Chromohalobacter salexigens (Target EFI-502114), with bound NA, ordered loop

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-octamer

Ligands

8 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: D.234, H.236, E.260, D.261, E.286 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.234 Water bridges: A:Y.182 NA.5: 5 residues within 4Å: Chain B: D.234, H.236, E.260, D.261, E.286 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.261 Water bridges: B:Y.182 NA.9: 5 residues within 4Å: Chain C: D.234, H.236, E.260, D.261, E.286 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.286 Water bridges: C:Y.182 NA.13: 5 residues within 4Å: Chain D: D.234, H.236, E.260, D.261, E.286 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.260 Water bridges: D:Y.182 NA.17: 5 residues within 4Å: Chain E: D.234, H.236, E.260, D.261, E.286 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.261, E:E.286 Water bridges: E:D.234, E:E.286 NA.21: 5 residues within 4Å: Chain F: D.234, H.236, E.260, D.261, E.286 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.261, F:E.286 Water bridges: F:D.234, F:E.286 NA.25: 5 residues within 4Å: Chain G: D.234, H.236, E.260, D.261, E.286 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:D.234, G:D.261 Water bridges: G:D.234, G:E.286 NA.29: 5 residues within 4Å: Chain H: D.234, H.236, E.260, D.261, E.286 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:D.261, H:E.286 Water bridges: H:D.234, H:E.286

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

CL.2: 9 residues within 4Å: Chain A: G.102, P.103, V.104, T.105 Chain H: G.102, P.103, V.104, T.105 Ligands: CL.30 Ligand excluded by PLIP CL.6: 9 residues within 4Å: Chain B: G.102, P.103, V.104, T.105 Chain G: G.102, P.103, V.104, T.105 Ligands: CL.26 Ligand excluded by PLIP CL.10: 9 residues within 4Å: Chain C: G.102, P.103, V.104, T.105 Chain F: G.102, P.103, V.104, T.105 Ligands: CL.22 Ligand excluded by PLIP CL.14: 9 residues within 4Å: Chain D: G.102, P.103, V.104, T.105 Chain E: G.102, P.103, V.104, T.105 Ligands: CL.18 Ligand excluded by PLIP CL.18: 9 residues within 4Å: Chain D: G.102, P.103, V.104, T.105 Chain E: G.102, P.103, V.104, T.105 Ligands: CL.14 Ligand excluded by PLIP CL.22: 9 residues within 4Å: Chain C: G.102, P.103, V.104, T.105 Chain F: G.102, P.103, V.104, T.105 Ligands: CL.10 Ligand excluded by PLIP CL.26: 9 residues within 4Å: Chain B: G.102, P.103, V.104, T.105 Chain G: G.102, P.103, V.104, T.105 Ligands: CL.6 Ligand excluded by PLIP CL.30: 9 residues within 4Å: Chain A: G.102, P.103, V.104, T.105 Chain H: G.102, P.103, V.104, T.105 Ligands: CL.2 Ligand excluded by PLIP

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: N.60, P.194, H.336, P.338, D.340, L.413 Chain H: Y.98, W.99 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: H.364, D.372, H.377, Y.379, F.381, F.386 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain B: N.60, P.194, H.336, P.338, D.340, L.413 Chain G: Y.98, W.99 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain B: H.364, D.372, H.377, Y.379, F.381, F.386 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain C: N.60, P.194, H.336, P.338, D.340, L.413 Chain F: Y.98, W.99 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain C: H.364, D.372, H.377, Y.379, F.381, F.386 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain D: N.60, P.194, H.336, P.338, D.340, L.413 Chain E: Y.98, W.99 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain D: H.364, D.372, H.377, Y.379, F.381, F.386 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain D: Y.98, W.99 Chain E: N.60, P.194, H.336, P.338, D.340, L.413 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain E: H.364, D.372, H.377, Y.379, F.381, F.386 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain C: Y.98, W.99 Chain F: N.60, P.194, H.336, P.338, D.340, L.413 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain F: H.364, D.372, H.377, Y.379, F.381, F.386 Ligand excluded by PLIP GOL.27: 8 residues within 4Å: Chain B: Y.98, W.99 Chain G: N.60, P.194, H.336, P.338, D.340, L.413 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain G: H.364, D.372, H.377, Y.379, F.381, F.386 Ligand excluded by PLIP GOL.31: 8 residues within 4Å: Chain A: Y.98, W.99 Chain H: N.60, P.194, H.336, P.338, D.340, L.413 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain H: H.364, D.372, H.377, Y.379, F.381, F.386 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Crystal structure of D-mannonate dehydratase homolog from Chromohalobacter salexigens (Target EFI-502114), with bound NA, ordered loop. to be published

Release Date

2012-06-27

Peptides

D-mannonate dehydratase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

D-mannonate dehydratase

Related Entries With Identical Sequence