SMTL ID : 1dog.1

REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: 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.1: 16 residues within 4Å: Chain A: W.169, N.170, T.172, S.183, Y.222, S.225, W.227, T.228, L.233, N.235, F.236, D.237, S.238, C.448, A.449, A.450 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.237, A:S.238, A:S.225 Water bridges: A:N.235, A:N.235, A:S.238, A:S.238, A:R.240, A:R.240

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.2: 16 residues within 4Å: Chain A: V.13, W.28, S.30, P.41, S.42, T.43, D.44, N.45, F.49, N.394, S.396, E.408, S.410, A.411, R.412, D.413 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.412, A:S.42, A:S.42, A:R.412, A:R.412, A:W.28 Water bridges: A:R.412, A:R.412, A:R.412, A:E.408, A:L.409, A:S.410, A:S.410, A:R.412

10 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.3: 7 residues within 4Å: Chain A: D.262, E.438, T.439, S.440, A.441, S.442, S.443 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.440, A:A.441, A:S.442, A:S.443 Water bridges: A:D.262, A:D.262, A:D.262, A:D.262, A:E.438 MAN.4: 3 residues within 4Å: Chain A: S.443, V.444, P.445 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.444 Water bridges: A:S.443 MAN.5: 3 residues within 4Å: Chain A: T.451, S.452 Ligands: MAN.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.452 Water bridges: A:Q.215 MAN.6: 4 residues within 4Å: Chain A: Q.167, T.451, S.452 Ligands: MAN.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.167, A:A.450 MAN.7: 4 residues within 4Å: Chain A: Q.167, S.454, G.455, Y.457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.167 Water bridges: A:Q.167 MAN.8: 4 residues within 4Å: Chain A: R.159, T.456, Y.457 Ligands: MAN.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.457 Water bridges: A:R.159, A:R.159 MAN.9: 6 residues within 4Å: Chain A: P.156, R.159, S.458, S.459 Ligands: MAN.8, MAN.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.159 Water bridges: A:E.152, A:E.152, A:S.458 MAN.10: 6 residues within 4Å: Chain A: A.86, I.87, G.90, S.459, V.460 Ligands: MAN.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.86, A:G.90 Water bridges: A:A.86, A:G.90, A:V.460, A:T.461 MAN.11: 6 residues within 4Å: Chain A: S.459, V.460, T.461 Ligands: MAN.9, MAN.10, MAN.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.459, A:S.459 MAN.12: 4 residues within 4Å: Chain A: E.152, T.461, T.463 Ligands: MAN.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.464

2 x NOJ: 1-DEOXYNOJIRIMYCIN(Non-covalent)

NOJ.13: 14 residues within 4Å: Chain A: A.39, Y.48, W.52, R.54, D.55, L.176, W.177, E.178, R.304, W.316, E.399, L.414, W.416 Ligands: NOJ.14 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.48, A:R.54, A:R.54, A:L.176, A:R.304 Water bridges: A:A.39, A:D.55, A:W.177, A:E.399 NOJ.14: 6 residues within 4Å: Chain A: W.177, E.178, E.179, R.304, Y.310 Ligands: NOJ.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.304, A:R.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harris, E.M. et al., Refined structure for the complex of 1-deoxynojirimycin with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution. Biochemistry (1993)

Release Date

1994-01-31

Peptides

GLUCOAMYLASE-471: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GLUCOAMYLASE-471

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