SMTL ID : 6i02.1

Structure of human D-glucuronyl C5 epimerase in complex with product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

1 x GNS- IDR- GNS- IDR- GNS- IDR- GNS- IDR: alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose

GNS-IDR-GNS-IDR-GNS-IDR-GNS-IDR.1: 29 residues within 4Å: Chain A: S.86, G.89, Y.90, N.91, V.94, R.95, R.97, Q.112, W.113, Y.120, I.122, Q.123, Q.126, K.278, R.338, L.340, M.355, E.409, Y.410, N.420, Y.424, Y.470, R.473, N.482, R.485, D.487, F.488, T.491 Chain B: N.527 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.89, A:N.91

1 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-MAN.2: 12 residues within 4Å: Chain A: K.134, N.135, E.138, K.139, I.143, V.145, T.148, N.303, T.305, H.311, M.312 Ligands: NAG-NAG-BMA.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.145, A:T.148

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.3: 9 residues within 4Å: Chain A: R.176, F.177, T.178, V.180, D.207, W.257, D.302, N.303 Ligands: NAG-NAG-BMA-MAN-NAG-MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.176, A:R.176

1 x IDR- GNS- IDR- GNS- IDR- GNS- IDR: alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid

IDR-GNS-IDR-GNS-IDR-GNS-IDR.4: 28 residues within 4Å: Chain A: N.527 Chain B: S.86, G.89, Y.90, N.91, V.94, R.95, R.97, Q.112, W.113, Y.120, I.122, Q.123, Q.126, R.338, L.340, M.355, E.409, Y.410, N.420, Y.424, Y.470, R.473, N.482, R.485, D.487, F.488, T.491 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.89, B:G.89, B:N.91

1 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.5: 10 residues within 4Å: Chain B: N.135, E.138, K.139, P.140, I.143, T.148, N.303, H.311, M.312 Ligands: NAG-NAG-BMA-MAN.6 No protein-ligand interaction detected (PLIP)

1 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.6: 8 residues within 4Å: Chain B: R.176, F.177, T.178, D.207, W.257, D.302, N.303 Ligands: NAG-NAG-BMA-MAN-MAN.5 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.7: 3 residues within 4Å: Chain B: L.211, N.213, T.255 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 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:T.148, A:E.150, A:N.179, A:D.302, H2O.5 CA.19: 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:D.302, B:D.302

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

NAG.9: 3 residues within 4Å: Chain A: L.211, T.212, N.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.212, A:N.213

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 8 residues within 4Å: Chain A: S.466, G.467, T.468, L.483, A.484, W.486, H.489 Chain B: R.523 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.523, A:T.468, A:T.468, A:T.468 GOL.11: 8 residues within 4Å: Chain A: S.102, G.103, V.104, G.106, R.254, T.259, T.261, R.262 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.254, A:R.254, A:T.259, A:T.261, A:R.262 Water bridges: A:V.104, A:E.105 GOL.12: 4 residues within 4Å: Chain A: K.403, H.404 Chain B: M.401, F.475 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.403, A:H.404, B:F.475 GOL.13: 8 residues within 4Å: Chain A: Y.127, H.131, I.203, T.261, R.262, D.263, A.310, A.314 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.263, A:A.310 Water bridges: A:Y.127, A:Y.127, A:H.131, A:A.310 GOL.14: 6 residues within 4Å: Chain A: N.91, E.93, V.94, D.263, V.265, T.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.91, A:N.91, A:D.263 Water bridges: A:D.263 GOL.15: 2 residues within 4Å: Chain A: Q.238, Y.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.238 GOL.16: 6 residues within 4Å: Chain A: K.403, H.404, D.405, R.450, E.453, S.454 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.405, A:D.405, A:S.454 GOL.20: 7 residues within 4Å: Chain B: Y.127, H.131, I.203, T.261, A.310, H.311, A.314 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.261, B:D.263, B:A.310, B:A.310, B:A.314 GOL.21: 5 residues within 4Å: Chain B: D.320, V.323, D.373, I.375, F.376 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.320, B:D.320, B:D.373 GOL.22: 6 residues within 4Å: Chain B: G.467, T.468, L.483, A.484, W.486, H.489 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.468, B:T.468, B:T.468, B:W.486 Water bridges: A:R.523 GOL.23: 9 residues within 4Å: Chain B: S.102, G.103, V.104, G.106, R.254, T.259, V.260, T.261, R.262 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.104, B:R.254, B:R.254, B:T.259, B:T.261, B:R.262, B:R.262

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.17: 9 residues within 4Å: Chain A: V.399, F.400, M.401, F.475, M.476 Chain B: K.403, H.404, A.457 Ligands: P6G.18 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:M.401, B:K.403 Water bridges: A:N.402, A:N.402 Salt bridges: B:K.403

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.18: 8 residues within 4Å: Chain A: M.476, L.477, G.478, I.479, A.480 Chain B: E.510, R.514 Ligands: MES.17 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.514, A:A.480

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

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