SMTL ID : 6epb.1

Structure of Chitinase 42 from Trichoderma harzianum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: W.131, E.171 Ligands: ACT.28 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.171, H2O.1, H2O.5, H2O.10, ACT.28 ZN.2: 1 residues within 4Å: Chain A: D.51 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.51, A:D.51, H2O.11 ZN.3: 3 residues within 4Å: Chain A: H.205, D.232 Ligands: ACT.30 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.205, A:D.232, H2O.10, ACT.30 ZN.4: 2 residues within 4Å: Chain A: H.395, G.399 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.395, H2O.1, H2O.10, H2O.11, H2O.11 ZN.5: 2 residues within 4Å: Chain A: H.92 Ligands: EDO.17 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.92, H2O.9, H2O.10 ZN.6: 2 residues within 4Å: Chain A: D.194, H.205 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.205, H2O.10, H2O.10 ZN.7: 3 residues within 4Å: Chain A: E.316 Ligands: ACT.31, IMD.32 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.316, H2O.9

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

EDO.8: 8 residues within 4Å: Chain A: S.41, H.66, I.68, L.125, T.209, Y.233, N.235, V.287 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: S.346 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: R.52, N.53, F.54, D.58, K.323 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: D.100, G.102, T.103, N.104, Y.106 Ligands: EDO.17 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: Y.93, A.94, D.95, Q.111, K.114 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: D.77, A.145, N.146, N.149 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: S.134, T.135, P.138, W.170, Y.172, Q.178 Ligand excluded by PLIP EDO.15: 1 residues within 4Å: Chain A: Q.405 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: K.110, L.422 Ligands: EDO.20, EDO.22 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: H.92, S.97, W.98, Y.106 Ligands: ZN.5, EDO.11 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: A.61, S.62, V.64, G.121, L.122, D.402, T.403 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain A: L.184, K.187 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: D.416, N.417, N.420, L.422, N.423 Ligands: EDO.16 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: N.73, L.74, W.133, S.134, T.135, N.136, F.137 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: D.95, K.110, K.114 Ligands: EDO.16 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: K.327, A.328, A.330, N.345, T.348, E.350 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain A: H.92, D.96, W.98 Ligands: EDO.25 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain A: H.92 Ligands: EDO.24 Ligand excluded by PLIP EDO.26: 1 residues within 4Å: Chain A: G.102 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain A: Y.50, D.51, R.52 Ligand excluded by PLIP

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

ACT.28: 7 residues within 4Å: Chain A: Y.43, D.169, E.171, M.237, Y.239, W.378 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.43, A:W.378 Hydrogen bonds: A:Y.239, A:Y.239 ACT.29: 2 residues within 4Å: Chain A: S.314, W.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.314 ACT.30: 5 residues within 4Å: Chain A: H.205, Q.229, V.230, D.232 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.190, A:Q.229 Salt bridges: A:H.205, A:K.285 ACT.31: 8 residues within 4Å: Chain A: T.45, W.47, R.52, E.316, W.378, E.379 Ligands: ZN.7, IMD.32 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.379 Water bridges: A:R.52 Salt bridges: A:R.52

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.32: 6 residues within 4Å: Chain A: Y.293, E.316, I.319, W.378 Ligands: ZN.7, ACT.31 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.295 Water bridges: A:E.316, A:E.316 pi-Stacking: A:Y.293, A:W.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kidibule, P.E. et al., Use of chitin and chitosan to produce new chitooligosaccharides by chitinase Chit42: enzymatic activity and structural basis of protein specificity. Microb. Cell Fact. (2018)

Release Date

2018-09-26

Peptides

Endochitinase 42: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endochitinase 42