SMTL ID : 8og4.1

Exostosin-like 3 UDP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: T.163, P.516, R.560, Y.561, N.564, L.585 Chain B: F.467, S.471 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.516 Hydrogen bonds: A:R.560 NAG-NAG.3: 8 residues within 4Å: Chain A: F.467, S.471 Chain B: T.163, P.516, R.560, Y.561, N.564, L.585 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.561 Hydrogen bonds: B:R.560

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 14 residues within 4Å: Chain A: D.751, H.754, S.756, W.757, L.758, Y.759, N.760, S.761, N.762, F.845, H.846, H.849, N.853 Chain B: A.615 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.751 NAG-NAG-BMA-MAN-MAN.4: 13 residues within 4Å: Chain A: A.615 Chain B: D.751, H.754, S.756, W.757, L.758, N.760, S.761, N.762, F.845, H.846, H.849, N.853 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.849, B:D.751, B:H.754

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

MN.5: 4 residues within 4Å: Chain A: R.644, D.716, D.718 Ligands: UDP.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.718, A:D.718 MN.7: 4 residues within 4Å: Chain B: R.644, D.716, D.718 Ligands: UDP.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.716, B:D.718, B:D.718

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

UDP.6: 13 residues within 4Å: Chain A: L.640, T.641, Y.642, R.644, N.669, N.695, L.697, R.700, D.716, D.717, D.718, I.801 Ligands: MN.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.642 Hydrogen bonds: A:Y.642, A:N.669, A:N.695, A:N.695, A:D.716, A:D.717, A:D.717 Salt bridges: A:R.644 UDP.8: 13 residues within 4Å: Chain B: L.640, T.641, Y.642, R.644, N.669, N.695, L.697, R.700, D.716, D.717, D.718, I.801 Ligands: MN.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.642 Hydrogen bonds: B:N.669, B:N.695, B:N.695, B:D.717, B:D.717 Salt bridges: B:R.644

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sammon, D. et al., Molecular mechanism of decision-making in glycosaminoglycan biosynthesis. Nat Commun (2023)

Release Date

2023-07-12

Peptides

Exostosin-like 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Exostosin-like 3

Related Entries With Identical Sequence