SMTL ID : 6txg.1

Proteinase K in complex with a "half sandwich"-type Ru(II) coordination compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

monomer

Ligands

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

NO3.1: 5 residues within 4Å: Chain A: M.55, V.56, K.57, T.58, S.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.57, A:S.63 Water bridges: A:T.58, A:T.58 NO3.2: 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 NO3.3: 8 residues within 4Å: Chain A: S.132, L.133, G.134, A.158, G.160, N.161, T.223, S.224 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.133, A:N.161, A:T.223, A:S.224 Water bridges: A:G.134, A:N.161, A:N.161, A:S.224

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

EDO.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.5: 7 residues within 4Å: Chain A: L.96, G.102, Y.104, I.107, L.133, G.134, G.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.102, A:G.134, A:G.134

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: P.175, V.177, D.200 Ligands: NYN.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:P.175, A:V.177, A:D.200, H2O.2, H2O.8

2 x NYN: chlorido(1,2-diaminoethane-k2N,N')(1,4,7-trithiacyclononane-k3S,S',S'')ruthenium(II) trifluoromethanesulfonate(Non-covalent)

NYN.7: 12 residues within 4Å: Chain A: P.175, S.176, V.177, C.178, S.197, V.198, L.199, D.200, C.249, R.250, V.269 Ligands: CA.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.175 Water bridges: A:V.177 Salt bridges: A:D.200, A:D.200, A:D.200 Metal complexes: A:D.200 NYN.9: 7 residues within 4Å: Chain A: T.16, S.17, P.18, N.257, K.258, D.260 Ligands: NA.8 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Water interactions Hydrogen bonds: A:K.258, A:D.260 Water bridges: A:K.258 Salt bridges: A:D.260, A:D.260, A:D.260 Metal complexes: A:D.260, H2O.9

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

NA.8: 3 residues within 4Å: Chain A: K.258, D.260 Ligands: NYN.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.258

1 x TFS: trifluoromethanesulfonic acid(Non-covalent)

TFS.10: 4 residues within 4Å: Chain A: R.189, N.263, I.264, P.265 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.266 Halogen bonds: A:R.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chiniadis, L. et al., High-resolution crystal structures of a "half sandwich"-type Ru(II) coordination compound bound to hen egg-white lysozyme and proteinase K. J.Biol.Inorg.Chem. (2020)

Release Date

2020-04-29

Peptides

Proteinase K: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Proteinase K

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