SMTL ID : 5a8m.1

Crystal structure of the selenomethionine derivative of beta-glucanase SdGluc5_26A from Saccharophagus degradans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-trimer

Ligands

9 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.3: 2 residues within 4Å: Chain A: R.69, N.100 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.17: 2 residues within 4Å: Chain B: H.303, I.304 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: R.69, N.100 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain C: T.191, T.192, R.200, F.230, N.231 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain C: H.303, I.304 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain C: R.69, N.100 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 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.10, H2O.11, H2O.11 MG.19: 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.26, H2O.27, H2O.27 MG.35: 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.41, H2O.41, H2O.42

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

SO4.5: 3 residues within 4Å: Chain A: E.125, R.128, W.129 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.125, A:E.125, A:E.125, A:W.129 Salt bridges: A:R.128 SO4.20: 3 residues within 4Å: Chain B: E.125, R.128, W.129 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.129 Salt bridges: B:R.128 SO4.36: 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

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: H.107, H.142, M.156, Y.157, W.330, W.336 Chain B: W.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.107, A:W.336 Water bridges: A:Y.157 GOL.7: 4 residues within 4Å: Chain A: P.37, R.169, F.173 Chain C: M.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.169 Water bridges: A:R.169 GOL.8: 6 residues within 4Å: Chain A: T.47, Q.48, S.49, F.50, D.61, P.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.48, A:D.61 Water bridges: A:K.46 GOL.21: 7 residues within 4Å: Chain B: H.107, M.156, Y.157, W.330, W.336 Chain C: W.32 Ligands: PGE.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.107, B:W.336 GOL.22: 4 residues within 4Å: Chain A: M.193 Chain B: P.37, R.169, F.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.169 Water bridges: B:R.169 GOL.37: 5 residues within 4Å: Chain B: M.193 Chain C: Y.36, 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.38: 6 residues within 4Å: Chain A: W.32 Chain C: H.107, M.156, Y.157, W.330, W.336 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:H.107, C:Y.157, A:W.32

22 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 B: K.162 Ligand excluded by PLIP PGE.10: 3 residues within 4Å: Chain A: G.194, N.195, R.200 Ligand excluded by PLIP PGE.11: 3 residues within 4Å: Chain A: W.85, H.122, E.125 Ligand excluded by PLIP PGE.12: 6 residues within 4Å: Chain A: Y.256, E.291, H.303, V.306, W.330, S.337 Ligand excluded by PLIP PGE.13: 3 residues within 4Å: Chain A: P.334, D.335, D.343 Ligand excluded by PLIP PGE.14: 3 residues within 4Å: Chain A: K.43, L.45, K.46 Ligand excluded by PLIP PGE.15: 3 residues within 4Å: Chain A: Y.217, K.221, E.247 Ligand excluded by PLIP PGE.23: 6 residues within 4Å: Chain B: R.112, D.158, T.159, T.160, E.163 Chain C: K.162 Ligand excluded by PLIP PGE.24: 3 residues within 4Å: Chain B: G.194, N.195, R.200 Ligand excluded by PLIP PGE.25: 3 residues within 4Å: Chain B: W.85, H.122, E.125 Ligand excluded by PLIP PGE.26: 7 residues within 4Å: Chain B: Y.256, E.291, H.303, V.306, W.330, S.337 Ligands: GOL.21 Ligand excluded by PLIP PGE.27: 4 residues within 4Å: Chain B: P.334, D.335, D.343, W.344 Ligand excluded by PLIP PGE.28: 5 residues within 4Å: Chain A: R.82, D.335 Chain B: D.30, W.32, D.33 Ligand excluded by PLIP PGE.29: 3 residues within 4Å: Chain B: Y.217, K.221, E.247 Ligand excluded by PLIP PGE.30: 6 residues within 4Å: Chain B: P.243, I.244, E.245, R.246, E.247, Y.285 Ligand excluded by PLIP PGE.31: 3 residues within 4Å: Chain B: P.262, E.263, N.269 Ligand excluded by PLIP PGE.39: 6 residues within 4Å: Chain A: K.162 Chain C: R.112, D.158, T.159, T.160, E.163 Ligand excluded by PLIP PGE.40: 3 residues within 4Å: Chain C: G.194, N.195, R.200 Ligand excluded by PLIP PGE.41: 4 residues within 4Å: Chain C: W.85, Q.86, H.122, E.125 Ligand excluded by PLIP PGE.42: 6 residues within 4Å: Chain C: Y.256, E.291, H.303, V.306, W.330, S.337 Ligand excluded by PLIP PGE.43: 5 residues within 4Å: Chain A: W.32, D.33 Chain C: K.78, R.82, D.335 Ligand excluded by PLIP PGE.44: 3 residues within 4Å: Chain C: P.334, D.335, D.343 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
B

C
C

PUTATIVE RETAINING B-GLYCOSIDASE

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