SMTL ID : 1gql.1

Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid and xylotriose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

2 x XYP- XYP: beta-D-xylopyranose-(1-1)-beta-D-xylopyranose(Non-covalent)

XYP-XYP.1: 11 residues within 4Å: Chain A: R.165, E.288, F.323, Y.325, R.332, D.361, H.517, Q.521, H.524, W.539 Ligands: BDP.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.288, A:R.332, A:R.332, A:Q.521 XYP-XYP.2: 11 residues within 4Å: Chain B: R.165, E.288, F.323, Y.325, R.332, D.361, H.517, Q.521, H.524, W.539 Ligands: BDP.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.288, B:Y.325, B:R.332, B:R.332, B:Q.521 Water bridges: B:Y.390

2 x BDP: beta-D-glucopyranuronic acid(Non-covalent)

BDP.3: 16 residues within 4Å: Chain A: W.156, E.164, R.165, V.206, N.207, K.284, E.288, R.321, F.323, K.356, D.361, E.389, Y.390, H.524 Ligands: XYP-XYP.1, XYP-XYP.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.164, A:R.165, A:R.165, A:N.207, A:Y.390, A:Y.390, A:Y.390 Water bridges: A:K.284 Salt bridges: A:K.284, A:R.321, A:K.356, A:K.356 BDP.13: 16 residues within 4Å: Chain B: W.156, E.164, R.165, V.206, N.207, K.284, E.288, R.321, F.323, K.356, D.361, E.389, Y.390, H.524 Ligands: XYP-XYP.2, XYP-XYP.2 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:E.164, B:E.164, B:R.165, B:R.165, B:N.207, B:Y.390, B:Y.390 Water bridges: B:K.284 Salt bridges: B:K.284, B:R.321, B:K.356, B:K.356

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 9 residues within 4Å: Chain A: Y.97, Y.122, H.126, R.129, S.195, L.196, G.197, W.467 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.97, A:R.129, A:R.129, A:S.195 EDO.5: 5 residues within 4Å: Chain A: R.47, P.184, T.187, D.188, R.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.47, A:R.47, A:R.191 EDO.6: 7 residues within 4Å: Chain A: H.126, R.129, S.144, R.464, W.467, I.471 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.126, A:R.129, A:R.464, A:R.464, A:W.467 EDO.7: 7 residues within 4Å: Chain A: Y.4, D.5, L.8, D.188, R.191, I.192, W.449 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.191, A:W.449 Water bridges: A:D.5, A:D.5, A:D.5, A:R.191 EDO.8: 4 residues within 4Å: Chain A: Q.623, D.627, K.642, Q.646 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.627, A:Q.646 Water bridges: A:D.627, A:K.642 EDO.14: 9 residues within 4Å: Chain B: Y.97, Y.122, H.126, R.129, S.195, L.196, G.197, W.467 Ligands: EDO.19 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.97, B:Y.97, B:R.129, B:R.129, B:S.195 EDO.15: 5 residues within 4Å: Chain B: R.47, P.184, T.187, D.188, R.191 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.47, B:R.47, B:R.191 Water bridges: B:T.187 EDO.16: 4 residues within 4Å: Chain B: N.555, T.557, H.590, H.591 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.590, B:H.591 Water bridges: B:N.555, B:H.591 EDO.17: 7 residues within 4Å: Chain B: Y.4, D.5, L.8, D.188, R.191, I.192, W.449 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.191, B:W.449 Water bridges: B:D.5, B:R.191 EDO.18: 2 residues within 4Å: Chain B: G.416, E.417 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.417 EDO.19: 8 residues within 4Å: Chain B: Y.97, H.126, R.129, S.144, R.464, W.467, I.471 Ligands: EDO.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.126, B:R.129, B:R.464, B:R.464, B:W.467

8 x CO: COBALT (II) ION(Non-covalent)

CO.9: 4 residues within 4Å: Chain A: M.498, A.621, M.622, T.625 No protein-ligand interaction detected (PLIP) CO.10: 5 residues within 4Å: Chain A: G.3, N.448, P.453, Q.456, R.637 No protein-ligand interaction detected (PLIP) CO.11: 3 residues within 4Å: Chain A: N.603, W.605, R.669 No protein-ligand interaction detected (PLIP) CO.12: 4 residues within 4Å: Chain A: N.158, N.160, V.162, W.698 No protein-ligand interaction detected (PLIP) CO.20: 4 residues within 4Å: Chain B: M.498, A.621, M.622, T.625 No protein-ligand interaction detected (PLIP) CO.21: 5 residues within 4Å: Chain B: G.3, N.448, P.453, Q.456, R.637 No protein-ligand interaction detected (PLIP) CO.22: 4 residues within 4Å: Chain B: N.158, N.160, V.162, W.698 No protein-ligand interaction detected (PLIP) CO.23: 3 residues within 4Å: Chain B: N.603, W.605, R.669 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nurizzo, D. et al., The Structural Basis for Catalysis and Specificity of the Pseudomonas Cellulosa Alpha-Glucuronidase, Glca67A. Structure (2002)

Release Date

2002-09-26

Peptides

ALPHA-D-GLUCURONIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ALPHA-D-GLUCURONIDASE

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