SMTL ID : 4d6h.1

Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 1 blood group A-tetrasaccharide (E558A X02 mutant)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x NAG- GAL- FUC- A2G: alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-FUC-A2G.1: 17 residues within 4Å: Chain A: Y.20, H.59, D.61, T.103, A.104, T.137, A.138, Y.140, W.141, T.206, W.239, Y.242, E.243, E.290, H.291, P.292, K.507 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.290, A:K.507, A:Y.20, A:Y.20, A:H.59, A:E.243, A:E.243, A:Y.140 Water bridges: A:K.507, A:K.507, A:K.507, A:K.507, A:K.204 Hydrophobic interactions: A:A.104, A:W.141, A:Y.140, A:W.141

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

EDO.2: 4 residues within 4Å: Chain A: Y.31, H.76, M.77, E.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.80 Water bridges: A:Y.31 EDO.7: 11 residues within 4Å: Chain A: G.211, N.212, D.213, S.214, G.346, F.349, V.350, T.354, R.356, E.357, T.359 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.213, A:S.214, A:S.214, A:G.346, A:T.354

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: P.47, K.311, R.315 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.311 Salt bridges: A:K.311, A:R.315 SO4.4: 3 residues within 4Å: Chain A: R.356, E.357, Q.358 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.357, A:E.357, A:Q.358, A:Q.358 SO4.5: 2 residues within 4Å: Chain A: S.403, T.404 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.404, A:T.404 Water bridges: A:S.403, A:T.404, A:Q.405, A:R.407 SO4.6: 1 residues within 4Å: Chain A: S.472 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.472 Water bridges: A:S.472, A:S.472, A:S.472, A:S.472

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwan, D.H. et al., Towards Efficient Enzymes for the Generation of Universal Blood Through Structure-Guided Directed Evolution. J.Am.Chem.Soc. (2015)

Release Date

2014-11-26

Peptides

GLYCOSIDE HYDROLASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GLYCOSIDE HYDROLASE