SMTL ID : 1kfg.1

The X-ray Crystal Structure of Cel9G from Clostridium cellulolyticum complexed with a Thio-Oligosaccharide Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x GS1- SGC- BGC- SGC: 4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-1-thio-beta-D-glucopyranose

GS1-SGC-BGC-SGC.1: 16 residues within 4Å: Chain A: D.58, H.125, Y.204, Y.205, S.208, W.254, C.257, W.258, D.259, D.260, F.309, W.311, R.315, E.420, Y.425 Ligands: TRS.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.316, A:Y.425, A:S.208, A:D.259, A:D.260 Water bridges: A:R.315, A:R.315 GS1-SGC-BGC-SGC.2: 12 residues within 4Å: Chain B: H.125, G.203, Y.204, Y.205, S.208, W.254, C.257, W.258, D.259, D.260, R.315, Y.425 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.259, B:H.316, B:Y.425, B:S.208, B:D.259, B:D.259, B:D.260

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.500, E.503, N.578, N.581, D.582 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.500, A:E.503, A:N.578, A:D.582, H2O.2 CA.4: 4 residues within 4Å: Chain A: S.209, D.212, D.213, D.259 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.209, A:D.212, A:D.212, A:D.213, A:D.259 CA.11: 5 residues within 4Å: Chain B: D.500, E.503, N.578, N.581, D.582 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.500, B:E.503, B:N.578, B:D.582, H2O.15 CA.12: 4 residues within 4Å: Chain B: S.209, D.212, D.213, D.259 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.209, B:D.212, B:D.212, B:D.213, B:D.259

5 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain A: H.371 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.371 MG.6: 1 residues within 4Å: Chain A: D.500 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.500, H2O.6, H2O.7, H2O.12, H2O.12 MG.7: 2 residues within 4Å: Chain A: D.24, L.25 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.24, H2O.4, H2O.12, H2O.12, H2O.12 MG.14: 2 residues within 4Å: Chain B: D.24, L.25 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.24, H2O.17, H2O.17, H2O.26, H2O.26, H2O.26 MG.15: 2 residues within 4Å: Chain B: E.79, D.80 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.79, H2O.18, H2O.18, H2O.21

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 7 residues within 4Å: Chain A: G.203, Y.204, Y.205, S.206, W.258 Ligands: GS1-SGC-BGC-SGC.1, GS1-SGC-BGC-SGC.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.203, A:G.203, A:S.206 Water bridges: A:S.206, A:D.259

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: H.371, T.386, T.389, E.412, I.413 Chain B: S.336 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.371, A:T.386, A:I.413, B:S.336 GOL.10: 4 residues within 4Å: Chain A: D.195, Y.198, S.206, S.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.206, A:S.207 GOL.16: 4 residues within 4Å: Chain B: H.371, T.389, E.412, I.413 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.371, B:I.413 Water bridges: B:N.414 GOL.17: 5 residues within 4Å: Chain B: K.193, Y.211, S.236, Y.237, N.240 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.236, B:N.240 Water bridges: B:Y.211, B:K.233

1 x NI: NICKEL (II) ION(Non-covalent)

NI.13: 1 residues within 4Å: Chain B: H.371 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:H.371, H2O.17, H2O.17, H2O.18, H2O.25, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mandelman, D. et al., The X-ray crystal structure of the multidomain endoglucanase Cel9G from Clostridium cellulolyticum complexed with natural and synthetic cello-olligosaccharides. J.Bacteriol. (2003)

Release Date

2003-07-15

Peptides

ENDOGLUCANASE G: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ENDOGLUCANASE G

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