SMTL ID : 5ccu.1

Crystal structure of endoglycoceramidase I from Rhodococ-cus equi

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 10 residues within 4Å: Chain A: E.222, P.223, E.267, P.268, N.269, V.270, W.272, N.273, P.298, H.299 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: V.89, R.90, F.432, V.433, S.434, D.435, R.458 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: I.41, T.42, D.53, R.57, V.59, H.133 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: A.38, T.39, P.40, I.41, T.128, A.129, G.131 Ligands: EDO.6 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: W.272, P.277, S.278, N.331, A.334, I.335, R.338 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: I.41, T.128, A.129, P.212 Ligands: EDO.4 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: A.443, V.444 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: D.68, Y.73, L.74, G.99, T.100, S.101, A.104, Y.116 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: F.170, P.171, E.222, V.270, N.273, Q.274 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: R.228, S.231, C.237, P.238, D.239, F.240 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: I.112, E.114, L.117, A.203, R.207 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain B: R.228, D.239, F.240, T.243 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain B: D.103, S.144, K.145, N.150, G.151, F.152 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: G.48, L.289, A.339, N.340, V.341 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: H.50, L.51, T.58, V.59, F.367, I.368 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: P.168, G.169, F.170, P.171, L.172 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: D.326, S.330, R.362, E.365, R.366 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: P.268, N.269, T.271, W.272, M.276, P.277, S.278 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: Q.245, Q.249, P.287, A.288, L.289, T.290, T.291 Ligand excluded by PLIP

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

NA.12: 3 residues within 4Å: Chain A: D.68, D.70, P.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, Y.B. et al., Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases. J. Biol. Chem. (2017)

Release Date

2015-09-02

Peptides

Putative secreted endoglycosylceramidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative secreted endoglycosylceramidase