SMTL ID : 6a9t.1

Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 58 residues deletion)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 7 residues within 4Å: Chain A: Y.240, D.271, D.282, S.284, E.411 Ligands: MN.2, GLY.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.271, A:D.271, A:D.282, A:E.411 MN.2: 7 residues within 4Å: Chain A: D.282, H.361, T.386, E.388, E.411 Ligands: MN.1, GLY.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.282, A:H.361, A:E.388, A:E.411, GLY.3

1 x GLY: GLYCINE(Non-covalent)

GLY.3: 10 residues within 4Å: Chain A: Y.240, D.271, D.282, H.361, H.368, E.388, E.411 Ligands: MN.1, MN.2, JEF.4 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.361, A:H.368

1 x JEF: O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500)(Non-covalent)

JEF.4: 12 residues within 4Å: Chain A: I.241, V.243, I.253, H.254, T.256, H.357, Y.358, H.361, H.368, E.388, R.409 Ligands: GLY.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.254 Water bridges: A:Y.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R. et al., Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function. FEBS Lett. (2019)

Release Date

2019-01-16

Peptides

Intermediate cleaving peptidase 55: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Intermediate cleaving peptidase 55

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