SMTL ID : 4v2x.1

High resolution structure of the full length tri-modular endo-beta-1, 4-glucanase B (Cel5B) from Bacillus halodurans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.216, D.217 Chain B: D.216, D.217 Ligands: CA.11 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.216, A:D.217, B:D.217, H2O.7, H2O.26 CA.2: 1 residues within 4Å: Chain A: F.467 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:F.467, H2O.15, H2O.16, H2O.16, H2O.20 CA.11: 5 residues within 4Å: Chain A: D.216, D.217 Chain B: D.216, D.217 Ligands: CA.1 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.216, B:D.217, A:D.217, H2O.7, H2O.26 CA.12: 1 residues within 4Å: Chain B: F.467 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:F.467, H2O.34, H2O.35, H2O.35, H2O.39

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

ACT.3: 5 residues within 4Å: Chain A: V.90, R.131, Q.134, V.135, W.138 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.134, A:V.135, A:W.138 Hydrogen bonds: A:V.90, A:V.90 Water bridges: A:R.89 ACT.13: 5 residues within 4Å: Chain B: V.90, R.131, Q.134, V.135, W.138 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Q.134, B:V.135, B:W.138 Hydrogen bonds: B:V.90, B:V.90 Water bridges: B:R.89

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: W.277, Q.522, E.529, Y.532 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.522, A:E.529 Water bridges: A:E.529, A:Y.532 GOL.5: 10 residues within 4Å: Chain A: N.282, G.330, V.331, I.332, Q.333, S.505, L.506, A.507, F.530, W.565 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.282, A:G.330, A:Q.333, A:S.505 Water bridges: A:T.287, A:L.506 GOL.6: 5 residues within 4Å: Chain A: W.157, E.160, N.164, G.167, K.171 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.160, A:N.164, A:K.171, A:K.171 Water bridges: A:Y.122, A:Y.122 GOL.7: 3 residues within 4Å: Chain A: A.284, G.285, Y.286 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.285 Water bridges: A:T.287, A:E.290, A:N.292 GOL.8: 2 residues within 4Å: Chain A: E.370, Q.374 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.370 Water bridges: A:E.370 GOL.9: 4 residues within 4Å: Chain A: Q.97, E.101, F.364, Y.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.97, A:T.368 GOL.14: 4 residues within 4Å: Chain B: W.277, Q.522, E.529, Y.532 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.522, B:E.529 Water bridges: B:E.529, B:Y.532 GOL.15: 10 residues within 4Å: Chain B: N.282, G.330, V.331, I.332, Q.333, S.505, L.506, A.507, F.530, W.565 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.282, B:G.330, B:Q.333, B:S.505 Water bridges: B:T.287, B:L.506 GOL.16: 5 residues within 4Å: Chain B: W.157, E.160, N.164, G.167, K.171 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.160, B:N.164, B:K.171, B:K.171 Water bridges: B:Y.122, B:Y.122 GOL.17: 3 residues within 4Å: Chain B: A.284, G.285, Y.286 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.285 Water bridges: B:T.287, B:E.290, B:N.292 GOL.18: 2 residues within 4Å: Chain B: E.370, Q.374 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.370 Water bridges: B:E.370 GOL.19: 4 residues within 4Å: Chain B: Q.97, E.101, F.364, Y.369 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.97, B:T.368

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.10: 3 residues within 4Å: Chain A: E.197, Y.274, D.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.197 Water bridges: A:Y.274 CAC.20: 3 residues within 4Å: Chain B: E.197, Y.274, D.326 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.197 Water bridges: B:Y.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Venditto, I. et al., Family 46 Carbohydrate-Binding Modules Contribute to the Enzymatic Hydrolysis of Xyloglucan and Beta-1,3-1,4-Glucans Through Distinct Mechanisms. J.Biol.Chem. (2015)

Release Date

2015-02-25

Peptides

ENDO-BETA-1,4-GLUCANASE (CELLULASE B): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ENDO-BETA-1,4-GLUCANASE (CELLULASE B)