SMTL ID : 6i01.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

BDP-GNS-BDP-GNS-BDP-GNS-BDP.1: 28 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, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.89 Water bridges: A:G.89 BDP-GNS-BDP-GNS-BDP-GNS-BDP.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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.86, B:G.89 Water bridges: B: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: 13 residues within 4Å: Chain A: N.135, E.138, K.139, P.140, I.143, V.145, T.148, R.152, N.303, T.305, H.311, M.312 Ligands: NAG-NAG-BMA-MAN-MAN.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.145, A:T.148, A:R.152

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.3: 10 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, NAG-NAG-BMA-MAN-NAG-MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175, A:R.176 NAG-NAG-BMA-MAN-MAN.6: 9 residues within 4Å: Chain B: R.176, F.177, T.178, D.207, W.257, D.302, N.303 Ligands: NAG-NAG-BMA-MAN-NAG.5, NAG-NAG-BMA-MAN-NAG.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.176

1 x NAG- NAG- BMA- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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.5: 13 residues within 4Å: Chain B: N.135, E.138, K.139, P.140, I.143, V.145, T.148, R.152, N.303, T.305, H.311, M.312 Ligands: NAG-NAG-BMA-MAN-MAN.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.303, B:T.148 Water bridges: B:N.303, B:N.303

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, T.212, N.213 No protein-ligand interaction detected (PLIP)

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

NAG.8: 4 residues within 4Å: Chain A: E.187, N.213, G.214, G.297 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.187 Hydrogen bonds: A:E.187, A:N.213

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain A: S.466, G.467, T.468, L.483, A.484, W.486, H.489 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.468, A:T.468 Water bridges: A:S.466, A:W.486, B:H.526 GOL.10: 9 residues within 4Å: Chain A: Y.127, H.131, I.203, T.261, R.262, D.263, A.310, A.313, A.314 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.263, A:A.314 Water bridges: A:E.93, A:Y.127, A:T.261, A:R.262, A:D.263, A:D.263 GOL.11: 8 residues within 4Å: Chain A: S.102, G.103, G.106, R.254, T.259, V.260, T.261, R.262 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.104, A:R.254, A:R.254, A:T.261, A:R.262 Water bridges: A:T.259, A:T.261 GOL.12: 5 residues within 4Å: Chain A: K.403, H.404 Chain B: M.401, F.475, M.476 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.403, A:H.404 GOL.13: 6 residues within 4Å: Chain A: I.251, G.252, P.253, R.254, T.255, S.256 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.254, A:T.255, A:T.255, A:T.255, A:S.256 GOL.14: 8 residues within 4Å: Chain A: L.461, D.463, I.469, H.474 Chain B: L.461, D.463, I.469, H.474 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.463, A:H.474 GOL.15: 5 residues within 4Å: Chain A: N.91, E.93, D.263, V.265, T.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.91, A:D.263, A:T.266, A:T.266 GOL.18: 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:W.486, B:H.489 Water bridges: A:R.523 GOL.19: 4 residues within 4Å: Chain B: D.320, D.373, I.375, F.376 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.320, B:D.373 GOL.20: 6 residues within 4Å: Chain B: E.93, Y.127, H.131, T.261, D.263, A.310 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.93, B:D.263, B:A.310 Water bridges: B:T.261 GOL.21: 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.261, B:T.261, B:R.262 Water bridges: B:T.261 GOL.22: 3 residues within 4Å: Chain B: R.75, A.76, V.83 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.75 GOL.23: 3 residues within 4Å: Chain B: K.329, F.389, Q.393 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.329, B:H.394 GOL.24: 6 residues within 4Å: Chain B: K.403, H.404, D.405, R.450, E.453, S.454 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.404, B:D.405, B:D.405, B:R.450, B:E.453, B:E.453

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

ACT.16: 3 residues within 4Å: Chain A: R.95, D.96, R.97 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.95 Hydrogen bonds: A:D.96, A:R.97 Salt bridges: A:R.97

2 x CA: CALCIUM ION(Non-covalent)

CA.17: 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.9 CA.25: 5 residues within 4Å: Chain B: T.148, E.150, T.178, N.179, D.302 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.150, B:T.178, B:N.179, B:D.302, H2O.17

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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