SMTL ID : 1on8.1 (1 other biounit)

Crystal structure of mouse alpha-1,4-N-acetylhexosaminyltransferase (EXTL2) with UDP and GlcUAb(1-3)Galb(1-O)-naphthalenelmethanol an acceptor substrate analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x GAL- BDP: beta-D-glucopyranuronic acid-(1-3)-beta-D-galactopyranose(Non-covalent)

GAL-BDP.1: 8 residues within 4Å: Chain A: R.144, Y.156, L.176, W.247, H.252, F.253, R.256 Ligands: UDP.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.144, A:Y.156, A:R.144 Water bridges: A:D.114, A:D.114, A:D.114, A:N.235, A:R.256 Salt bridges: A:R.144, A:H.252, A:R.256 GAL-BDP.2: 8 residues within 4Å: Chain B: R.144, Y.156, L.176, W.247, H.252, F.253, R.256 Ligands: UDP.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.144, B:R.144, B:R.144 Water bridges: B:D.114 Salt bridges: B:R.144, B:H.252, B:R.256

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 2 residues within 4Å: Chain A: D.116 Ligands: UDP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.116, H2O.1, H2O.1, H2O.1 MN.6: 3 residues within 4Å: Chain B: D.116, E.237 Ligands: UDP.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.116, H2O.3, H2O.3, H2O.3

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.4: 17 residues within 4Å: Chain A: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, D.114, D.115, D.116, Y.243, G.245, M.246, W.247, H.252 Ligands: GAL-BDP.1, MN.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.37, A:Y.243 Hydrogen bonds: A:Q.35, A:Y.37, A:R.39, A:N.64, A:N.93, A:N.93, A:D.115, A:D.115, A:Y.243, A:Y.243, A:M.246, A:W.247 Water bridges: A:R.39, A:R.39, A:D.114, A:D.114 Salt bridges: A:R.39 UDP.7: 19 residues within 4Å: Chain B: Q.35, T.36, Y.37, R.39, N.64, N.93, M.95, R.98, D.114, D.115, D.116, Q.205, E.237, G.245, M.246, W.247, H.252 Ligands: GAL-BDP.2, MN.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.37 Hydrogen bonds: B:Q.35, B:Y.37, B:N.64, B:N.93, B:N.93, B:R.98, B:D.114, B:D.115, B:D.115, B:Q.205, B:E.237, B:M.246, B:W.247 Water bridges: B:R.39, B:R.39, B:R.256 Salt bridges: B:R.39

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

EDO.5: 6 residues within 4Å: Chain A: F.134, Q.137, P.223, I.226, I.277 Chain B: Q.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.137 Water bridges: A:G.225 EDO.8: 6 residues within 4Å: Chain A: Q.133 Chain B: F.134, Q.137, P.223, I.226, I.277 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.137 Water bridges: B:Q.137, B:K.222, B:G.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedersen, L.C. et al., Crystal structure of an alpha-1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis. J.Biol.Chem. (2003)

Release Date

2003-04-22

Peptides

Alpha-1,4-N-acetylhexosaminyltransferase EXTL2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-1,4-N-acetylhexosaminyltransferase EXTL2

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