SMTL ID : 5hq1.1

Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamics of cisplatin binding to histidine in a protein Struct. Dyn. 1, 034701 (2014) regarding the refinement of 4mwk, 4mwm, 4mwn and 4oxe and the method we have adopted.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

monomer

Ligands

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

DMS.1: 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

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: N.65, D.66, G.67, R.68, T.69, S.72 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Ligands: PT.8, CL.12 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: H.15, V.92, N.93, K.96 Ligands: PT.8, CL.9 Ligand excluded by PLIP

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

NO3.3: 6 residues within 4Å: Chain A: Y.53, N.65, D.66, P.79, C.80, S.81 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.80, A:S.81 Water bridges: A:R.68, A:R.68, A:S.81, A:S.81 NO3.4: 1 residues within 4Å: Chain A: E.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.7, A:E.7 NO3.10: 6 residues within 4Å: Chain A: S.24, L.25, G.26, V.120, Q.121, I.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.24, A:G.26, A:Q.121 NO3.11: 2 residues within 4Å: Chain A: R.112, K.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.116, A:K.116

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

PT.5: 4 residues within 4Å: Chain A: H.15, T.89 Ligands: PT.6, PT.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.15 PT.6: 4 residues within 4Å: Chain A: R.14, H.15 Ligands: PT.5, PT.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.15 PT.7: 3 residues within 4Å: Chain A: H.15 Ligands: PT.5, PT.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.15 PT.8: 3 residues within 4Å: Chain A: H.15 Ligands: CL.9, CL.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanley, S.W. et al., Comment on "Structural dynamics of cisplatin binding to histidine in a protein" [Struct. Dyn. 1, 034701 (2014)]. Struct Dyn (2016)

Release Date

2016-05-18

Peptides

Lysozyme C: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysozyme C

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