SMTL ID : 7aua.1

Cryo-EM structure of human exostosin-like 3 (EXTL3) in complex with UDP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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: 2 residues within 4Å: Chain A: Y.560, N.563 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.560 NAG-NAG.3: 2 residues within 4Å: Chain B: Y.560, N.563 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.560

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.2: 11 residues within 4Å: Chain A: D.750, H.753, S.755, W.756, L.757, N.759, S.760, N.761, F.844, H.848, N.852 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.750, A:H.753, A:S.755, A:W.756, A:H.848 NAG-NAG-BMA-MAN.4: 11 residues within 4Å: Chain B: D.750, H.753, S.755, W.756, L.757, N.759, S.760, N.761, F.844, H.848, N.852 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.750, B:H.753, B:S.755, B:W.756, B:H.848

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

MN.5: 2 residues within 4Å: Chain A: D.717 Ligands: UDP.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.717, A:D.717 MN.7: 2 residues within 4Å: Chain B: D.717 Ligands: UDP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.717, B:D.717

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

UDP.6: 12 residues within 4Å: Chain A: L.639, T.640, Y.641, R.643, N.668, N.694, L.696, D.715, D.716, D.717, I.800 Ligands: MN.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.639, A:N.668, A:N.694, A:N.694, A:D.716 Salt bridges: A:R.643, A:R.829 UDP.8: 12 residues within 4Å: Chain B: L.639, T.640, Y.641, R.643, N.668, N.694, L.696, D.715, D.716, D.717, I.800 Ligands: MN.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.639, B:N.668, B:N.694, B:N.694, B:D.716 Salt bridges: B:R.643, B:R.829

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilson, L.F.L. et al., The structure of EXTL3 helps to explain the different roles of bi-domain exostosins in heparan sulfate synthesis. Nat Commun (2022)

Release Date

2022-05-18

Peptides

Exostosin-like 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Exostosin-like 3

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