SMTL ID : 5a95.1

Crystal structure of beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with tetrasaccharide A, form 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-trimer

Ligands

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

BGC-BGC-BGC.1: 16 residues within 4Å: Chain A: H.107, H.142, I.144, M.156, Y.157, N.188, E.189, Q.291, Y.300, H.303, V.306, W.330, D.335, W.336, S.337 Chain C: W.32 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Water bridges: C:W.32, A:S.337 Hydrogen bonds: A:Y.300, A:D.335, A:S.337 BGC-BGC-BGC.2: 17 residues within 4Å: Chain A: W.32, D.33 Chain B: H.107, H.142, I.144, M.156, Y.157, N.188, E.189, Y.256, Q.291, Y.300, H.303, W.330, D.335, W.336, S.337 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.337 BGC-BGC-BGC.3: 15 residues within 4Å: Chain B: W.32 Chain C: H.107, H.142, I.144, M.156, Y.157, N.188, E.189, Q.291, H.303, V.306, W.330, D.335, W.336, S.337 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain C Water bridges: B:W.32, C:Y.300, C:S.337, C:S.337, C:S.337 Hydrogen bonds: C:D.335, C:D.335, C:S.337

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

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.7, H2O.8, H2O.15 MG.10: 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.29, H2O.31, H2O.37 MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 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.49, H2O.50, H2O.58

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

CL.5: 5 residues within 4Å: Chain A: T.191, T.192, R.200, F.230, N.231 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: K.221, E.247 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: N.201, W.202 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: H.303, I.304 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: T.191, T.192, R.200, F.230, N.231 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: R.246, E.247 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: P.35, Y.36 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: E.125, R.128, W.129 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain C: T.191, T.192, R.200, F.230, N.231 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: R.246, E.247 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: R.200, N.201, W.202 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain C: K.87, R.128, W.129 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: R.169, M.215, S.219 Chain B: T.196 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.196 Water bridges: A:S.219

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

TRS.17: 2 residues within 4Å: Chain C: S.88, E.91 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.91 Water bridges: C:K.87, C:K.87, C:S.88, C:S.88

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

Related Entries With Identical Sequence