SMTL ID : 5a8o.1

Crystal structure of beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with cellotetraose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x BGC- BGC- BGC- BGC: beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-BGC-BGC-BGC.1: 17 residues within 4Å: Chain A: H.107, I.144, Q.153, M.156, Y.157, E.189, W.232, Y.256, K.259, K.261, Q.291, P.305, W.330, W.336, S.337 Chain C: W.32, Y.36 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.107, A:Y.157, A:W.336, A:S.337, A:S.337, A:S.337 BGC-BGC-BGC-BGC.15: 17 residues within 4Å: Chain A: W.32, Y.36 Chain B: H.107, I.144, Q.153, M.156, Y.157, E.189, W.232, Y.256, K.259, K.261, Q.291, P.305, W.330, W.336, S.337 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.107, B:Y.157, B:W.336, B:S.337, B:S.337, B:S.337 BGC-BGC-BGC-BGC.29: 17 residues within 4Å: Chain B: W.32, Y.36 Chain C: H.107, I.144, Q.153, M.156, Y.157, E.189, W.232, Y.256, K.259, K.261, Q.291, P.305, W.330, W.336, S.337 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.107, C:W.336, C:S.337, C:S.337, C:S.337 Water bridges: C:Y.157

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: T.191, T.192, R.200, F.230, N.231 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: T.191, T.192, R.200, F.230, N.231 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain C: T.191, T.192, R.200, F.230, N.231 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: V.178, V.181, V.223 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:V.178, A:V.181, H2O.7, H2O.7, H2O.7 MG.17: 3 residues within 4Å: Chain B: V.178, V.181, V.223 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:V.178, B:V.181, H2O.18, H2O.18, H2O.18 MG.31: 3 residues within 4Å: Chain C: V.178, V.181, V.223 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:V.178, C:V.181, H2O.29, H2O.29, H2O.29

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: A.302, H.303, I.304, K.307 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.302, A:I.304 Water bridges: A:K.307, A:K.307 Salt bridges: A:H.303, A:K.307 SO4.5: 3 residues within 4Å: Chain A: E.125, R.128, W.129 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.125 Salt bridges: A:R.128 SO4.18: 4 residues within 4Å: Chain B: A.302, H.303, I.304, K.307 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.302, B:I.304 Water bridges: B:K.307, B:K.307 Salt bridges: B:H.303, B:K.307 SO4.19: 3 residues within 4Å: Chain B: E.125, R.128, W.129 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.125 Salt bridges: B:R.128 SO4.32: 4 residues within 4Å: Chain C: A.302, H.303, I.304, K.307 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.302, C:I.304 Water bridges: C:K.307, C:K.307 Salt bridges: C:H.303, C:K.307 SO4.33: 3 residues within 4Å: Chain C: E.125, R.128, W.129 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.125 Salt bridges: C:R.128

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: P.37, R.169, F.173 Chain B: M.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.169 Water bridges: A:R.169 GOL.7: 4 residues within 4Å: Chain A: R.82, D.335 Chain C: W.32, D.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.82, A:R.82 GOL.8: 4 residues within 4Å: Chain A: T.47, Q.48, F.50, D.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.48, A:D.61 GOL.20: 4 residues within 4Å: Chain B: P.37, R.169, F.173 Chain C: M.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.169 Water bridges: B:R.169 GOL.21: 4 residues within 4Å: Chain A: W.32, D.33 Chain B: R.82, D.335 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.82, B:R.82 GOL.22: 4 residues within 4Å: Chain B: T.47, Q.48, F.50, D.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.48, B:D.61 GOL.34: 4 residues within 4Å: Chain A: M.193 Chain C: P.37, R.169, F.173 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.169 Water bridges: C:R.169 GOL.35: 4 residues within 4Å: Chain B: W.32, D.33 Chain C: R.82, D.335 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.82, C:R.82 GOL.36: 4 residues within 4Å: Chain C: T.47, Q.48, F.50, D.61 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.48, C:D.61

18 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 6 residues within 4Å: Chain A: R.112, D.158, T.159, T.160, E.163 Chain C: K.162 Ligand excluded by PLIP PGE.10: 4 residues within 4Å: Chain A: W.85, Q.86, H.122, E.125 Ligand excluded by PLIP PGE.11: 2 residues within 4Å: Chain A: G.194, R.200 Ligand excluded by PLIP PGE.12: 1 residues within 4Å: Chain A: D.298 Ligand excluded by PLIP PGE.13: 6 residues within 4Å: Chain A: P.243, I.244, E.245, R.246, E.247, Y.285 Ligand excluded by PLIP PGE.14: 7 residues within 4Å: Chain A: W.32, D.33, I.34, P.35, Y.36 Chain B: H.154, M.156 Ligand excluded by PLIP PGE.23: 6 residues within 4Å: Chain A: K.162 Chain B: R.112, D.158, T.159, T.160, E.163 Ligand excluded by PLIP PGE.24: 4 residues within 4Å: Chain B: W.85, Q.86, H.122, E.125 Ligand excluded by PLIP PGE.25: 2 residues within 4Å: Chain B: G.194, R.200 Ligand excluded by PLIP PGE.26: 1 residues within 4Å: Chain B: D.298 Ligand excluded by PLIP PGE.27: 6 residues within 4Å: Chain B: P.243, I.244, E.245, R.246, E.247, Y.285 Ligand excluded by PLIP PGE.28: 7 residues within 4Å: Chain B: W.32, D.33, I.34, P.35, Y.36 Chain C: H.154, M.156 Ligand excluded by PLIP PGE.37: 6 residues within 4Å: Chain B: K.162 Chain C: R.112, D.158, T.159, T.160, E.163 Ligand excluded by PLIP PGE.38: 4 residues within 4Å: Chain C: W.85, Q.86, H.122, E.125 Ligand excluded by PLIP PGE.39: 2 residues within 4Å: Chain C: G.194, R.200 Ligand excluded by PLIP PGE.40: 1 residues within 4Å: Chain C: D.298 Ligand excluded by PLIP PGE.41: 6 residues within 4Å: Chain C: P.243, I.244, E.245, R.246, E.247, Y.285 Ligand excluded by PLIP PGE.42: 7 residues within 4Å: Chain A: H.154, M.156 Chain C: W.32, D.33, I.34, P.35, Y.36 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lafond, M. et al., The Quaternary Structure of a Glycoside Hydrolase Dictates Specificity Towards Beta-Glucans. J.Biol.Chem. (2016)

Release Date

2016-01-20

Peptides

PUTATIVE RETAINING B-GLYCOSIDASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

PUTATIVE RETAINING B-GLYCOSIDASE

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