SMTL ID : 3ch0.1

Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 12 residues within 4Å: Chain A: H.14, R.15, E.41, D.43, H.56, E.136, K.138, F.176, L.196, E.198, W.242 Ligands: GOL.18 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.242, A:W.242 Hydrogen bonds: A:E.136, A:K.138, A:E.198 Water bridges: A:R.15, A:R.18, A:E.41, A:Q.174 Salt bridges: A:H.14, A:H.14, A:R.15, A:H.56, A:H.56, A:K.138, A:K.138

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: H.61, H.62, E.63, R.103 Ligands: GOL.18 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: E.198, D.220, T.222, L.223 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: D.220, V.221, W.242, T.243 Ligands: EDO.3, EDO.7, EDO.8 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: L.207, E.208, L.210, S.211, F.212, T.213 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: M.67, E.93, I.94, D.95 Ligands: EDO.16 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: T.243, V.244, N.245, E.249 Ligands: EDO.4, EDO.8 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: R.18, R.103, T.243, N.245, D.264 Ligands: EDO.4, EDO.7 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: D.156, V.159, A.160, K.163, Y.188 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: L.153, D.156, L.157, A.160 Ligands: EDO.9 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: E.251, T.252 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: M.66, M.67, D.72 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: L.20, K.31 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: S.8, D.10, T.38, Q.132 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: P.102, R.103, F.104, K.105, S.106, Y.265 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: E.93, D.95, V.113 Ligands: EDO.6 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: E.208, K.209, L.210, S.211 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 6 residues within 4Å: Chain A: R.15, R.18, H.56, R.103 Ligands: CIT.1, EDO.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:R.18, A:R.18, A:H.56, A:R.103, A:R.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution. To be published

Release Date

2008-03-18

Peptides

Glycerophosphodiester phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycerophosphodiester phosphodiesterase