SMTL ID : 5a8n.1

Crystal structure of the native form of beta-glucanase SdGluc5_26A from Saccharophagus degradans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: T.191, T.192, R.200, F.230, N.231 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: H.303, I.304 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: T.191, T.192, R.200, F.230, N.231 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: H.303, I.304 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain C: T.191, T.192, R.200, F.230, N.231 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain C: H.303, I.304 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: V.178, V.181 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.14: 2 residues within 4Å: Chain B: V.178, V.181 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:V.178, B:V.181, H2O.19, H2O.19, H2O.19 MG.25: 2 residues within 4Å: Chain C: V.178, V.181 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:V.178, C:V.181, H2O.31, H2O.31, H2O.31

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

SO4.4: 3 residues within 4Å: Chain A: E.125, R.128, W.129 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.129 Salt bridges: A:R.128 SO4.15: 3 residues within 4Å: Chain B: E.125, R.128, W.129 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.129 Salt bridges: B:R.128 SO4.26: 3 residues within 4Å: Chain C: E.125, R.128, W.129 2 PLIP interactions: 2 interactions with chain C Water bridges: C:W.129 Salt bridges: C:R.128

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: H.107, M.156, Y.157, W.330, W.336 Chain B: W.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.107, A:Y.157 GOL.6: 5 residues within 4Å: Chain A: D.30, W.32, D.33 Chain C: R.82, D.335 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:W.32, C:R.82 GOL.16: 6 residues within 4Å: Chain B: H.107, M.156, Y.157, W.330, W.336 Chain C: W.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.107 GOL.17: 5 residues within 4Å: Chain A: R.82, D.335 Chain B: D.30, W.32, D.33 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.32, A:R.82 GOL.27: 6 residues within 4Å: Chain A: W.32 Chain C: H.107, M.156, Y.157, W.330, W.336 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.107 GOL.28: 5 residues within 4Å: Chain B: R.82, D.335 Chain C: D.30, W.32, D.33 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.82, C:W.32

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

PGE.7: 6 residues within 4Å: Chain A: R.112, D.158, T.159, T.160, E.163 Chain B: K.162 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.162, A:T.159 PGE.8: 6 residues within 4Å: Chain A: Y.256, E.291, H.303, V.306, W.330, S.337 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.291 PGE.9: 2 residues within 4Å: Chain A: G.194, R.200 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.200, A:R.200 Water bridges: A:G.194, A:G.194, A:N.195 PGE.10: 2 residues within 4Å: Chain A: R.169, F.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.169, A:R.169 PGE.11: 3 residues within 4Å: Chain A: W.232, K.259, P.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.259, A:K.259 PGE.18: 6 residues within 4Å: Chain B: R.112, D.158, T.159, T.160, E.163 Chain C: K.162 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.162, B:T.159 PGE.19: 6 residues within 4Å: Chain B: Y.256, E.291, H.303, V.306, W.330, S.337 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.256, B:E.291 PGE.20: 2 residues within 4Å: Chain B: G.194, R.200 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.200, B:R.200 Water bridges: B:G.194, B:G.194, B:N.195 PGE.21: 2 residues within 4Å: Chain B: R.169, F.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.169, B:R.169 PGE.22: 3 residues within 4Å: Chain B: W.232, K.259, P.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.259, B:K.259 PGE.29: 6 residues within 4Å: Chain A: K.162 Chain C: R.112, D.158, T.159, T.160, E.163 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.162, C:T.159 PGE.30: 6 residues within 4Å: Chain C: Y.256, E.291, H.303, V.306, W.330, S.337 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.291 PGE.31: 2 residues within 4Å: Chain C: G.194, R.200 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.200, C:R.200 Water bridges: C:G.194, C:G.194, C:N.195 PGE.32: 2 residues within 4Å: Chain C: R.169, F.173 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.169, C:R.169 PGE.33: 3 residues within 4Å: Chain C: W.232, K.259, P.305 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.259, C:K.259

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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