SMTL ID : 3hn3.1

Human beta-glucuronidase at 1.7 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- GUP: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-L-gulopyranose-(1-2)-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-MAN-MAN-MAN-MAN-MAN-GUP.1: 16 residues within 4Å: Chain A: N.34, R.36, V.76, G.77, W.78, Y.109, N.153, T.155, T.157, T.165, I.166, Q.167, Y.168, K.177, G.178, Q.396 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.168, A:Q.396 Hydrogen bonds: A:T.165, A:Q.167, A:Q.396, A:R.36, A:Y.168, A:Y.168

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- BMA: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-2)-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-MAN-MAN-MAN-MAN-MAN-BMA.2: 19 residues within 4Å: Chain B: D.33, N.34, R.35, R.36, V.76, G.77, W.78, Y.109, N.153, T.155, T.157, P.158, T.165, I.166, Q.167, Y.168, K.177, G.178, Q.396 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.167, B:Q.396, B:R.36, B:Y.168, B:Y.168 Water bridges: B:Q.396, B:Q.396 Hydrophobic interactions: B:R.35

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN-MAN-MAN-MAN-MAN.3: 16 residues within 4Å: Chain C: D.33, N.34, R.36, V.76, G.77, W.78, Y.109, N.153, T.155, T.157, P.158, T.165, I.166, Y.168, G.178, Q.396 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Y.168 Hydrogen bonds: C:R.36, C:Y.168

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN-MAN-MAN.4: 18 residues within 4Å: Chain D: D.33, N.34, R.36, V.76, G.77, W.78, Y.109, N.153, T.155, T.157, T.165, I.166, Q.167, Y.168, K.177, G.178, Q.396 Ligands: BMA.12 4 PLIP interactions: 4 interactions with chain D Water bridges: D:Y.168 Hydrogen bonds: D:R.36, D:Y.168, D:Y.168, D:Y.168

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

NAG.5: 3 residues within 4Å: Chain A: N.252, G.253, T.254 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.254 Hydrogen bonds: A:N.252 NAG.7: 2 residues within 4Å: Chain B: N.252, G.253 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.252 Water bridges: B:N.252 NAG.9: 2 residues within 4Å: Chain C: N.252, G.253 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.252, C:N.252 NAG.11: 3 residues within 4Å: Chain D: N.252, G.253, T.254 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.252 Water bridges: D:N.252, D:G.253, D:T.254

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 9 residues within 4Å: Chain A: S.463, N.464, S.465, L.481, N.482, S.483, Y.485, Q.504, W.508 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.481, A:Q.504 Hydrogen bonds: A:Y.485, A:W.508 Water bridges: A:Y.467, A:N.482, A:Y.484, A:H.489 MRD.10: 8 residues within 4Å: Chain C: S.463, N.464, S.465, L.481, N.482, Y.485, Q.504, W.508 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.481, C:Q.504, C:W.508 Hydrogen bonds: C:W.508 Water bridges: C:Y.467 MRD.14: 1 residues within 4Å: Chain D: Y.475 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.475

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 9 residues within 4Å: Chain B: S.463, N.464, S.465, L.481, N.482, S.483, Y.485, Q.504, W.508 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.481, B:Q.504, B:W.508 Hydrogen bonds: B:Y.485, B:W.508 Water bridges: B:Y.467 MPD.13: 8 residues within 4Å: Chain D: S.463, N.464, S.465, L.481, N.482, Y.485, Q.504, W.508 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.481, D:L.481, D:Q.504, D:W.508 Hydrogen bonds: D:W.508 Water bridges: D:S.465, D:W.508

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.12: 3 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klei, H.E. et al., Human beta-glucuronidasel at 1.7 A resolution. To be Published

Release Date

2009-12-01

Peptides

Beta-glucuronidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

Beta-glucuronidase

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