SMTL ID : 3i10.1

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (NP_812074.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.35 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: R.28, S.29, A.30, D.94, K.95, D.96 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.28, A:D.94 Water bridges: A:K.95, A:K.95 Salt bridges: A:K.95 ACT.2: 3 residues within 4Å: Chain A: T.100, N.101, Y.102 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.102 Hydrogen bonds: A:N.101 Water bridges: A:V.99

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

EDO.3: 3 residues within 4Å: Chain A: T.35, V.103, E.109 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: L.175, N.177, N.205, P.206, L.207 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: D.202, K.204 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: T.5, I.6, T.9, L.19, D.47, H.277, N.278 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: P.243, Y.266, D.269, Y.270, K.273 Ligands: EDO.16 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: G.150, V.172, D.174 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: N.16, I.251, R.257, W.276 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: R.24, W.27, E.32, R.71 Ligands: EDO.11 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: P.31, E.32, T.72, K.93, D.94, K.95 Ligands: EDO.10 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: P.203, G.232, N.233, H.234, L.238 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: P.13, K.14 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: P.13, K.14, S.15, F.216, K.217, R.257 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: K.76, G.77, W.82 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: Y.266, D.269 Ligands: EDO.7 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: D.174, I.199, S.229 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: K.7, N.143, K.166, L.168 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: Q.54, K.55, K.80, I.128 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: T.68, E.78 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.21: 8 residues within 4Å: Chain A: D.123, K.148, V.172, E.197, I.199, N.224, L.226, Q.260 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.148, A:N.224, A:Q.260 Water bridges: A:D.123, A:D.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (NP_812074.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.35 A resolution. To be Published

Release Date

2009-07-21

Peptides

Putative Glycerophosphoryl diester phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative Glycerophosphoryl diester phosphodiesterase