SMTL ID : 6hzz.1

Structure of human D-glucuronyl C5 epimerase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 12 residues within 4Å: Chain A: N.135, E.138, K.139, P.140, P.141, I.143, V.145, T.148, N.303, H.311, M.312 Ligands: NAG-NAG-BMA-MAN-MAN.2 No protein-ligand interaction detected (PLIP)

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: 8 residues within 4Å: Chain A: R.176, F.177, T.178, D.207, W.257, D.302, N.303 Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 7 residues within 4Å: Chain B: R.176, F.177, T.178, D.207, W.257, D.302, N.303 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 8 residues within 4Å: Chain B: N.135, E.138, K.139, P.140, P.141, I.143, H.311, M.312 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.4: 3 residues within 4Å: Chain B: L.211, N.213, T.255 No protein-ligand interaction detected (PLIP)

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

NAG.6: 4 residues within 4Å: Chain A: E.187, N.213, G.214, G.297 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.187 Hydrogen bonds: A:E.187

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 4 residues within 4Å: Chain A: D.48, R.485, W.486 Chain B: H.526 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.486 Water bridges: A:D.48 Salt bridges: B:H.526

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 5 residues within 4Å: Chain A: Q.112, R.338, Y.410, Y.470, Y.488 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.112, A:Y.410, A:Y.470, B:N.527 Salt bridges: A:R.338 SO4.11: 4 residues within 4Å: Chain B: R.338, Y.410, Y.470, Y.488 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.410, B:Y.470, B:Y.488, A:N.527 Salt bridges: B:R.338

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain A: T.148, E.150, T.178, N.179, D.302 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.150, A:T.178, A:N.179, A:D.302, H2O.1 CA.12: 5 residues within 4Å: Chain B: T.148, E.150, T.178, N.179, D.302 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.148, B:E.150, B:T.178, B:N.179, B:D.302

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain A: Y.90, N.91, R.95 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: Y.90, N.91, R.95 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Debarnot, C. et al., Substrate binding mode and catalytic mechanism of human heparan sulfate d-glucuronyl C5 epimerase. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-04-03

Peptides

D-glucuronyl C5-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-glucuronyl C5-epimerase