SMTL ID : 2zut.2 (1 other biounit)

Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GalNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.1: 10 residues within 4Å: Chain A: V.162, Y.165, F.218, W.233, F.310, L.311, G.312, D.313, H.460 Chain B: S.612 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.310 Hydrogen bonds: A:D.313, A:D.313, A:D.313, B:S.612 Water bridges: A:E.228, A:S.336, A:S.336, A:H.460, B:S.612 A2G.5: 11 residues within 4Å: Chain A: S.612 Chain B: V.162, Y.165, F.218, W.233, F.310, L.311, G.312, D.313, S.336, H.460 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.310 Hydrogen bonds: B:D.313, B:D.313, B:D.313, A:S.612 Water bridges: B:E.228, B:S.336, B:S.336, B:H.460, A:S.612

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: W.447, G.448, K.449, M.450, S.488, D.491 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.449, A:M.450, A:S.488, A:D.491 Water bridges: A:W.447 GOL.3: 5 residues within 4Å: Chain A: V.116, R.118, G.121, R.257, E.259 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:F.551 Hydrogen bonds: A:R.257, A:R.257 GOL.6: 6 residues within 4Å: Chain B: W.447, G.448, K.449, M.450, S.488, D.491 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.449, B:K.449, B:M.450, B:S.488, B:S.488 Water bridges: B:K.322, B:K.322, B:K.449 GOL.7: 5 residues within 4Å: Chain B: V.116, R.118, G.121, R.257, E.259 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:F.551, A:F.551 Hydrogen bonds: B:R.257, B:R.257

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 1 residues within 4Å: Chain A: D.174 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.174, H2O.9, H2O.16, H2O.18, H2O.26, H2O.31 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain B: K.229 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hidaka, M. et al., The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold. J.Biol.Chem. (2009)

Release Date

2008-12-30

Peptides

Lacto-N-biose phosphorylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Lacto-N-biose phosphorylase

Related Entries With Identical Sequence