SMTL ID : 4yeo.1

Triclinic HEWL co-crystallised with cisplatin, studied at a data collection temperature of 150K - new refinement

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.98 Å

Oligo State

monomer

Ligands

1 x CPT: Cisplatin(Non-covalent)

CPT.1: 3 residues within 4Å: Chain A: R.14, H.15 Ligands: PT.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Water bridges: A:I.88 Metal complexes: A:H.15, H2O.5

4 x PT: PLATINUM (II) ION(Non-covalent)

PT.2: 2 residues within 4Å: Chain A: H.15 Ligands: CPT.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.15 PT.3: 2 residues within 4Å: Chain A: H.15, N.93 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.15, H2O.5 PT.4: 2 residues within 4Å: Chain A: K.116 Ligands: NO3.10 No protein-ligand interaction detected (PLIP) PT.5: 1 residues within 4Å: Chain A: K.1 No protein-ligand interaction detected (PLIP)

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

EDO.6: 3 residues within 4Å: Chain A: N.113, R.114, T.118 No protein-ligand interaction detected (PLIP)

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 7 residues within 4Å: Chain A: Q.57, I.58, N.59, W.63, I.98, A.107, W.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.59 pi-Cation interactions: A:W.108 DMS.8: 4 residues within 4Å: Chain A: N.65, D.66, G.67 Ligands: NO3.9 No protein-ligand interaction detected (PLIP)

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

NO3.9: 7 residues within 4Å: Chain A: Y.53, N.65, D.66, P.79, C.80, S.81 Ligands: DMS.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.80, A:S.81 Water bridges: A:R.68, A:S.81, A:S.81 NO3.10: 2 residues within 4Å: Chain A: K.116 Ligands: PT.4 No protein-ligand interaction detected (PLIP) NO3.11: 1 residues within 4Å: Chain A: Q.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.41, A:Q.41 NO3.12: 3 residues within 4Å: Chain A: G.16, Y.20, K.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.96, A:K.96 NO3.13: 2 residues within 4Å: Chain A: R.45, R.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.45, A:R.68 Water bridges: A:R.68 NO3.14: 1 residues within 4Å: Chain A: E.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.7, A:E.7 NO3.15: 2 residues within 4Å: Chain A: Q.121, R.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.125, A:R.125 Water bridges: A:G.126

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

ACT.16: 2 residues within 4Å: Chain A: W.62, R.73 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shabalin, I. et al., Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-03-04

Peptides

Lysozyme C: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysozyme C