SMTL ID : 5hmv.1

Re refinement of 4mwk.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.98 Å

Oligo State

monomer

Ligands

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

DMS.1: 5 residues within 4Å: Chain A: N.65, D.66, G.67 Ligands: NO3.15, NO3.16 No protein-ligand interaction detected (PLIP) DMS.2: 3 residues within 4Å: Chain A: R.5, A.122, W.123 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.123 DMS.13: 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

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

NO3.3: 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 NO3.4: 3 residues within 4Å: Chain A: D.87, T.89 Ligands: PT.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.89 Water bridges: A:D.87, A:D.87 NO3.5: 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 NO3.6: 1 residues within 4Å: Chain A: E.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.7, A:E.7 NO3.14: 6 residues within 4Å: Chain A: S.24, L.25, G.26, V.120, Q.121, I.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.24, A:G.26, A:V.120, A:Q.121 NO3.15: 6 residues within 4Å: Chain A: N.65, N.74, N.77, I.78, P.79 Ligands: DMS.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.65, A:N.74 NO3.16: 7 residues within 4Å: Chain A: Y.53, N.65, D.66, P.79, C.80, S.81 Ligands: DMS.1 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

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

PT.7: 7 residues within 4Å: Chain A: R.14, H.15 Ligands: PT.8, PT.9, CL.17, PT.18, CL.19 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.15 PT.8: 5 residues within 4Å: Chain A: H.15 Ligands: PT.7, PT.9, CL.17, PT.18 No protein-ligand interaction detected (PLIP) PT.9: 9 residues within 4Å: Chain A: H.15, T.89 Ligands: NO3.4, PT.7, PT.8, PT.11, CL.17, PT.18, CL.19 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.15 PT.10: 3 residues within 4Å: Chain A: H.15, N.93 Ligands: PT.11 No protein-ligand interaction detected (PLIP) PT.11: 4 residues within 4Å: Chain A: H.15 Ligands: PT.9, PT.10, PT.18 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.15, A:H.15 PT.12: 1 residues within 4Å: Chain A: K.1 No protein-ligand interaction detected (PLIP) PT.18: 7 residues within 4Å: Chain A: H.15 Ligands: PT.7, PT.8, PT.9, PT.11, CL.17, CL.19 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.15

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

CL.17: 6 residues within 4Å: Chain A: R.14 Ligands: PT.7, PT.8, PT.9, PT.18, CL.19 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain A: H.15 Ligands: PT.7, PT.9, CL.17, PT.18 Ligand excluded by PLIP

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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