SMTL ID : 5avk.1

Crystal structure of proteinase K from Engyodontium album

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 5 residues within 4Å: Chain A: Y.60, Y.61, K.94, D.97, D.98 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.94, A:D.98 Water bridges: A:Y.61, A:Y.61, A:R.64, A:D.98 NO3.2: 8 residues within 4Å: Chain A: S.132, L.133, G.134, A.158, G.160, N.161, T.223, S.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.132, A:N.161 Water bridges: A:S.224, A:S.224 NO3.3: 3 residues within 4Å: Chain A: D.165, R.167, N.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.167, A:N.168 Water bridges: A:D.165, A:D.165 NO3.4: 4 residues within 4Å: Chain A: D.184, R.185, Y.186, R.188 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.188, A:D.207 Water bridges: A:R.185, A:R.185, A:R.185, A:R.188

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.188, R.189, N.263 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.263 Water bridges: A:D.184, A:R.188, A:R.189, A:R.189

2 x PR: PRASEODYMIUM ION(Non-covalent)

PR.6: 3 residues within 4Å: Chain A: P.175, V.177, D.200 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.175, A:V.177, A:D.200, A:D.200, H2O.1 PR.7: 2 residues within 4Å: Chain A: T.16, D.260 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.16, H2O.8, H2O.9, H2O.10, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yazawa, K. et al., Derivatization of Proteinase K with Heavy Atoms Enhances Its Thermal Stability. Acs Catalysis (2016)

Release Date

2016-07-06

Peptides

Proteinase K: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Proteinase K

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