SMTL ID : 7sck.1

Cryo-EM structure of the human Exostosin-1 and Exostosin-2 heterodimer in complex with a 7-sugar oligosaccharide acceptor analog

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain B: W.393, P.569, N.593, F.640, G.641, T.642, P.644 No protein-ligand interaction detected (PLIP)

1 x NDG- BDP- NDG- BDP: beta-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-BDP-NDG-BDP.2: 13 residues within 4Å: Chain A: Q.706, V.707, S.708 Chain B: R.525, Y.538, S.540, E.541, W.542, L.550, K.607, K.609, M.626, R.629 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.525, B:Y.538, B:K.609, B:K.609, B:S.540, B:S.540 Salt bridges: B:R.525, B:H.625, B:R.629

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

UDP.3: 12 residues within 4Å: Chain A: K.241, G.242, K.243, Y.245, R.254, Y.293, Y.298, G.313, S.318, F.319, R.320, E.323 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.241, A:K.243, A:K.243, A:Y.245, A:R.254, A:Y.293, A:S.318, A:S.318, A:E.323 Salt bridges: A:K.243, A:K.243, A:R.254, A:R.320, A:R.320 pi-Stacking: A:Y.298 UDP.5: 12 residues within 4Å: Chain B: L.417, T.418, Y.419, R.421, N.446, N.473, L.475, D.494, D.495, D.496, M.580 Ligands: MN.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.421, B:N.446, B:N.473, B:N.473, B:D.494, B:D.495, B:D.495 Salt bridges: B:R.421

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

NAG.4: 4 residues within 4Å: Chain A: K.235, Y.236, E.300, N.304 No protein-ligand interaction detected (PLIP)

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

MN.6: 2 residues within 4Å: Chain B: D.496 Ligands: UDP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.496

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Structural basis for heparan sulfate co-polymerase action by the EXT1-2 complex. Nat.Chem.Biol. (2023)

Release Date

2022-09-28

Peptides

Exostosin-1: A
Exostosin-2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Exostosin-1

Exostosin-2

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