SMTL ID : 4bf7.1

Emericilla nidulans endo-beta-1,4-galactanase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

15 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: E.292, V.346, D.349 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.292, A:E.292, A:D.349, H2O.7 ZN.2: 3 residues within 4Å: Chain A: D.334, D.337 Ligands: ACT.20 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.334, A:D.337, A:D.337 ZN.3: 5 residues within 4Å: Chain A: I.31, E.32, S.35, W.317, D.319 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.32, A:D.319, H2O.1, H2O.1 ZN.4: 2 residues within 4Å: Chain A: H.167, D.169 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.167, A:D.169, A:D.169, H2O.4 ZN.5: 3 residues within 4Å: Chain A: K.183, I.193, T.222 No protein-ligand interaction detected (PLIP) ZN.6: 4 residues within 4Å: Chain A: D.300, D.304 Ligands: ACT.26, ACT.27 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.300, A:D.300, A:D.304, A:D.304 ZN.7: 7 residues within 4Å: Chain A: N.152, E.153, S.230, Y.232, E.263 Ligands: ACT.17, GOL.24 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.153, A:E.263 ZN.8: 1 residues within 4Å: Chain A: H.160 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.160, H2O.7, H2O.7 ZN.9: 2 residues within 4Å: Chain A: H.176 Ligands: IMD.23 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.176, H2O.4 ZN.10: 3 residues within 4Å: Chain A: D.34 Ligands: ACT.18, ACT.25 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.34, A:D.34 ZN.11: 2 residues within 4Å: Chain A: D.105, D.108 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.105, A:D.108, H2O.3, H2O.3, H2O.3 ZN.12: 4 residues within 4Å: Chain A: D.202, D.204, A.205 Ligands: ACT.21 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.202, A:D.202, H2O.5, H2O.5 ZN.13: 3 residues within 4Å: Chain A: A.18, A.299, E.303 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.303, H2O.1, H2O.7, H2O.7, H2O.7 ZN.14: 1 residues within 4Å: Chain A: H.167 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.167, H2O.4, H2O.7, H2O.7 ZN.15: 2 residues within 4Å: Chain A: D.119, D.121 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.119, A:D.119, H2O.3

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

NAG.16: 4 residues within 4Å: Chain A: T.122, W.125, Q.126, N.129 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.125, A:Q.126

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

ACT.17: 9 residues within 4Å: Chain A: E.153, D.198, S.230, Y.232, Y.235, E.263 Ligands: ZN.7, ACT.19, GOL.24 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.232, A:Y.235 Hydrogen bonds: A:S.230 Water bridges: A:Y.232 ACT.18: 7 residues within 4Å: Chain A: L.30, E.33, D.34, E.81, R.85 Ligands: ZN.10, ACT.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.30, A:E.33 Hydrogen bonds: A:D.34 Water bridges: A:R.85 ACT.19: 5 residues within 4Å: Chain A: P.106, D.198, N.199, Y.235 Ligands: ACT.17 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.235 Hydrogen bonds: A:N.199 Water bridges: A:N.199, A:N.199, A:W.201, A:Y.235 ACT.20: 6 residues within 4Å: Chain A: D.334, D.337, T.339, V.340, R.341 Ligands: ZN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.340 ACT.21: 5 residues within 4Å: Chain A: W.201, D.202, D.204, A.205 Ligands: ZN.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.204 Hydrogen bonds: A:D.204 ACT.22: 1 residues within 4Å: Chain A: D.238 No protein-ligand interaction detected (PLIP) ACT.25: 5 residues within 4Å: Chain A: L.30, D.34, Y.78 Ligands: ZN.10, ACT.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.78 ACT.26: 5 residues within 4Å: Chain A: D.300, E.303, D.304 Ligands: ZN.6, ACT.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.303 Hydrogen bonds: A:D.304 ACT.27: 6 residues within 4Å: Chain A: K.245, D.300, T.301, D.304 Ligands: ZN.6, ACT.26 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.245 ACT.28: 4 residues within 4Å: Chain A: K.183, D.184, S.185, S.186 No protein-ligand interaction detected (PLIP) ACT.29: 2 residues within 4Å: Chain A: D.289, T.293 No protein-ligand interaction detected (PLIP)

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.23: 5 residues within 4Å: Chain A: H.176, G.217, T.218, L.220 Ligands: ZN.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.176

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 13 residues within 4Å: Chain A: R.62, H.98, W.103, A.104, D.105, N.152, E.153, H.196, Y.232, E.263, W.313 Ligands: ZN.7, ACT.17 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.152, A:E.153, A:E.263 Water bridges: A:R.62, A:Y.232, A:Y.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Otten, H. et al., The Binding of Zinc Ions to Emericella Nidulans Endo-[Beta]-1,4-Galactanase is Essential for Crystal Formation. Acta Crystallogr.,Sect.F (2013)

Release Date

2013-08-07

Peptides

ARABINOGALACTAN ENDO-1,4-BETA-GALACTOSIDASE A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ARABINOGALACTAN ENDO-1,4-BETA-GALACTOSIDASE A