SMTL ID : 8viw.1

Cryo-EM structure of heparosan synthase 2 from Pasteurella multocida with polysaccharide in the GlcNAc-T active site

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

BDP-GNS-BDP-GNS-BDP.1: 17 residues within 4Å: Chain A: H.416, I.418, R.432, V.434, S.436, F.437, Y.438, K.439, D.477, Y.512 Chain B: A.86, N.87, T.88, T.89, S.90 Ligands: MN.5, UDP.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.432, A:D.477, A:D.477, A:R.432 Salt bridges: A:H.416, A:R.432, A:R.432 BDP-GNS-BDP-GNS-BDP.2: 17 residues within 4Å: Chain A: A.86, N.87, T.88, T.89, S.90 Chain B: H.416, I.418, R.432, V.434, S.436, F.437, Y.438, K.439, D.477, Y.512 Ligands: MN.9, UDP.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.432, B:D.477, B:D.477, B:R.432 Salt bridges: B:H.416, B:R.432, B:R.432 BDP-GNS-BDP-GNS-BDP.3: 17 residues within 4Å: Chain C: H.416, I.418, R.432, V.434, S.436, F.437, Y.438, K.439, D.477, Y.512 Chain D: A.86, N.87, T.88, T.89, S.90 Ligands: MN.13, UDP.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.432, C:D.477, C:R.432, C:Y.438, C:Y.512 Salt bridges: C:H.416, C:R.432, C:R.432 BDP-GNS-BDP-GNS-BDP.4: 17 residues within 4Å: Chain C: A.86, N.87, T.88, T.89, S.90 Chain D: H.416, I.418, R.432, V.434, S.436, F.437, Y.438, K.439, D.477, Y.512 Ligands: MN.17, UDP.18 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.432, D:D.477, D:R.432, D:Y.438, D:Y.512 Salt bridges: D:H.416, D:R.432, D:R.432

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

MN.5: 3 residues within 4Å: Chain A: D.389 Ligands: BDP-GNS-BDP-GNS-BDP.1, UDP.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.389 MN.7: 3 residues within 4Å: Chain A: D.125, D.126 Ligands: UDP.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.125, A:D.125, H2O.1 MN.9: 3 residues within 4Å: Chain B: D.389 Ligands: BDP-GNS-BDP-GNS-BDP.2, UDP.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.389 MN.11: 3 residues within 4Å: Chain B: D.125, D.126 Ligands: UDP.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.125, B:D.125, H2O.1 MN.13: 3 residues within 4Å: Chain C: D.389 Ligands: BDP-GNS-BDP-GNS-BDP.3, UDP.14 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.389 MN.15: 3 residues within 4Å: Chain C: D.125, D.126 Ligands: UDP.16 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.125, C:D.125, H2O.1 MN.17: 3 residues within 4Å: Chain D: D.389 Ligands: BDP-GNS-BDP-GNS-BDP.4, UDP.18 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.389 MN.19: 3 residues within 4Å: Chain D: D.125, D.126 Ligands: UDP.20 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.125, D:D.125, H2O.1

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

UDP.6: 15 residues within 4Å: Chain A: C.306, S.307, I.308, R.311, D.334, R.363, D.364, D.387, D.388, D.389, T.510, L.511, Y.512 Ligands: BDP-GNS-BDP-GNS-BDP.1, MN.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.308, A:L.511 Hydrogen bonds: A:I.308, A:R.311, A:D.334, A:D.334, A:D.388, A:D.388, A:L.511, A:Y.512 Salt bridges: A:R.311 UDP.8: 19 residues within 4Å: Chain A: T.42, S.43, H.44, T.46, D.72, N.100, G.102, T.103, D.123, S.124, D.125, R.155, N.225, R.228, S.231, L.232, F.233, K.293 Ligands: MN.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.232 Hydrogen bonds: A:T.42, A:H.44, A:H.44, A:D.72, A:N.100, A:S.124, A:S.124, A:D.125, A:L.232, A:F.233 Water bridges: A:R.155, A:R.155 Salt bridges: A:R.155, A:R.228 UDP.10: 15 residues within 4Å: Chain B: C.306, S.307, I.308, R.311, D.334, R.363, D.364, D.387, D.388, D.389, T.510, L.511, Y.512 Ligands: BDP-GNS-BDP-GNS-BDP.2, MN.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.308, B:L.511 Hydrogen bonds: B:I.308, B:R.311, B:D.334, B:D.334, B:D.388, B:D.388, B:L.511, B:Y.512 Salt bridges: B:R.311 UDP.12: 19 residues within 4Å: Chain B: T.42, S.43, H.44, T.46, D.72, N.100, G.102, T.103, D.123, S.124, D.125, R.155, N.225, R.228, S.231, L.232, F.233, K.293 Ligands: MN.11 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.232 Hydrogen bonds: B:T.42, B:H.44, B:H.44, B:D.72, B:N.100, B:S.124, B:S.124, B:D.125, B:L.232, B:F.233 Water bridges: B:R.155, B:R.155 Salt bridges: B:R.155, B:R.228 UDP.14: 15 residues within 4Å: Chain C: C.306, S.307, I.308, R.311, D.334, R.363, D.364, D.387, D.388, D.389, T.510, L.511, Y.512 Ligands: BDP-GNS-BDP-GNS-BDP.3, MN.13 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.308, C:L.511 Hydrogen bonds: C:I.308, C:R.311, C:D.334, C:D.388, C:D.388, C:D.388, C:L.511, C:Y.512 Salt bridges: C:R.311 UDP.16: 19 residues within 4Å: Chain C: T.42, S.43, H.44, T.46, D.72, N.100, G.102, T.103, D.123, S.124, D.125, R.155, N.225, R.228, S.231, L.232, F.233, K.293 Ligands: MN.15 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.232 Hydrogen bonds: C:T.42, C:H.44, C:H.44, C:D.72, C:D.72, C:N.100, C:S.124, C:S.124, C:D.125, C:L.232, C:F.233 Water bridges: C:R.155, C:R.155 Salt bridges: C:R.155, C:R.228 UDP.18: 15 residues within 4Å: Chain D: C.306, S.307, I.308, R.311, D.334, R.363, D.364, D.387, D.388, D.389, T.510, L.511, Y.512 Ligands: BDP-GNS-BDP-GNS-BDP.4, MN.17 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.308, D:L.511 Hydrogen bonds: D:I.308, D:R.311, D:D.334, D:D.388, D:D.388, D:D.388, D:L.511, D:Y.512 Salt bridges: D:R.311 UDP.20: 19 residues within 4Å: Chain D: T.42, S.43, H.44, T.46, D.72, N.100, G.102, T.103, D.123, S.124, D.125, R.155, N.225, R.228, S.231, L.232, F.233, K.293 Ligands: MN.19 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.232 Hydrogen bonds: D:T.42, D:H.44, D:H.44, D:D.72, D:D.72, D:N.100, D:S.124, D:S.124, D:D.125, D:N.225, D:L.232, D:F.233 Water bridges: D:R.155, D:R.155 Salt bridges: D:R.155, D:R.228

Links

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Citation

Stancanelli, E. et al., Structural and Functional Analysis of Heparosan Synthase 2 from Pasteurella multocida to Improve the Synthesis of Heparin. Acs Catalysis (2024)

Release Date

2024-07-24

Peptides

Heparosan synthase B: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Heparosan synthase B