SMTL ID : 8p1g.1

Crystal structure of inactive TtCE16 in complex with acetate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: G.52, F.59, Y.275, S.291, L.292, N.293, N.305 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.292 Hydrogen bonds: A:L.292 Water bridges: A:N.293

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.2: 3 residues within 4Å: Chain A: N.207, T.209, E.210 No protein-ligand interaction detected (PLIP)

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.3: 11 residues within 4Å: Chain A: D.22, G.24, R.25, L.26, G.27, T.46, T.48, T.49, A.50, H.276, Y.298 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.22, A:D.22, A:D.22, A:G.24, A:L.26, A:G.27, A:A.50, A:A.50, A:G.52, A:H.276, A:Y.298

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: N.255, Y.258, N.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.259 Water bridges: A:E.181 PEG.16: 5 residues within 4Å: Chain A: Y.264, L.265, D.266, N.293, K.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.264, A:K.306 Water bridges: A:N.293 PEG.21: 5 residues within 4Å: Chain A: D.162, Y.165, K.166, R.239, W.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PEG.22: 4 residues within 4Å: Chain A: Q.81, I.82, K.148, D.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.148

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

ACT.5: 8 residues within 4Å: Chain A: D.18, A.19, Y.20, S.74, G.75, T.131, N.132, H.302 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.19, A:Y.20, A:T.131 Hydrogen bonds: A:A.19, A:G.75, A:N.132 Salt bridges: A:H.302 ACT.7: 3 residues within 4Å: Chain A: E.227, D.249 Ligands: ACT.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.249 Water bridges: A:T.327 ACT.25: 7 residues within 4Å: Chain A: D.249, S.252, K.324, Y.325 Ligands: EDO.6, ACT.7, EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.325 Hydrogen bonds: A:S.252, A:S.252

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: S.252, N.255, D.256 Ligands: EDO.8, ACT.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.255, A:D.256 Water bridges: A:S.252 EDO.8: 5 residues within 4Å: Chain A: D.256, K.324, Y.325 Ligands: EDO.6, ACT.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.256 Water bridges: A:S.252 EDO.9: 3 residues within 4Å: Chain A: V.109, R.118, T.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.109, A:R.118, A:T.167 EDO.10: 3 residues within 4Å: Chain A: P.268, H.269, N.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.269, A:N.270 EDO.12: 4 residues within 4Å: Chain A: S.155, F.158, M.233, R.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.239, A:R.239 Water bridges: A:S.155 EDO.13: 2 residues within 4Å: Chain A: R.92 Ligands: EDO.26 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.92, A:R.92, A:D.100 EDO.14: 1 residues within 4Å: Chain A: E.190 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain A: D.196, N.201, T.202, T.204, K.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.204, A:K.205 EDO.17: 4 residues within 4Å: Chain A: Y.165, K.166, G.168, R.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.168, A:R.170, A:R.170 EDO.18: 1 residues within 4Å: Chain A: L.89 No protein-ligand interaction detected (PLIP) EDO.19: 1 residues within 4Å: Chain A: L.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.113 EDO.20: 4 residues within 4Å: Chain A: G.33, I.90, N.91, R.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.90 EDO.24: 1 residues within 4Å: Chain A: K.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.237, A:K.237 EDO.26: 3 residues within 4Å: Chain A: D.99, D.100 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.99 Water bridges: A:R.92

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.11: 1 residues within 4Å: Chain A: N.91 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.91

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.23: 5 residues within 4Å: Chain A: P.39, P.103, Q.106, A.107, L.110 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pentari, C. et al., The role of CE16 exo-deacetylases in hemicellulolytic enzyme mixtures revealed by the biochemical and structural study of the novel TtCE16B esterase. Carbohydr Polym (2024)

Release Date

2024-03-20

Peptides

Carbohydrate esterase family 16 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Carbohydrate esterase family 16 protein