SMTL ID : 5lvk.1

Human Lysozyme co-crystallized with [H2Ind][trans-RuCl4(DMSO)(HInd)]

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: N.66, S.80 Chain B: T.43 Ligands: NA.8 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.66, A:S.80, B:T.43 Water bridges: A:C.81 SO4.2: 4 residues within 4Å: Chain A: N.88, A.90 Chain B: K.1, V.2 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.2, A:N.88 Water bridges: B:K.1 SO4.3: 5 residues within 4Å: Chain A: Y.20, K.97 Chain B: R.5, K.33, Y.38 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.33, A:K.97

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

CL.4: 3 residues within 4Å: Chain A: N.60, W.64, W.109 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain B: R.115 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: R.119 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: Q.126, G.127 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: W.64, W.109 Ligand excluded by PLIP

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

NA.8: 5 residues within 4Å: Chain A: N.66, N.75 Chain B: N.44, Y.45 Ligands: SO4.1 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.66, A:N.75, B:Y.45 Water bridges: B:T.43, B:T.43 NA.9: 4 residues within 4Å: Chain A: C.77, R.98 Chain B: S.36, G.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.77 NA.13: 3 residues within 4Å: Chain B: N.88, A.90, D.91 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.88, B:N.88, B:D.91 Water bridges: B:D.91, B:A.92

2 x RU: RUTHENIUM ION(Non-covalent)

RU.10: 3 residues within 4Å: Chain B: R.107, R.113, Q.117 No protein-ligand interaction detected (PLIP) RU.11: 1 residues within 4Å: Chain B: G.127 No protein-ligand interaction detected (PLIP)

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

NO3.14: 1 residues within 4Å: Chain B: R.119 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oszajca, M. et al., Ligand-dependent interaction of anticancer ruthenium complexes with hen egg white lysozyme and human lysozyme. To Be Published

Release Date

2016-09-28

Peptides

Lysozyme C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysozyme C

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