SMTL ID : 3dmz.1

Hexafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: R.125, W.126, D.127, E.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.125, A:W.126, A:D.127, A:E.128, A:E.128 PO4.2: 2 residues within 4Å: Chain A: N.144, R.148 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.144 Water bridges: A:R.145, A:R.148, A:R.148, A:R.148, A:R.148, A:R.148 Salt bridges: A:R.148

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

CL.3: 1 residues within 4Å: Chain A: G.56 Ligand excluded by PLIP

1 x HFB: hexafluorobenzene(Non-covalent)

HFB.4: 12 residues within 4Å: Chain A: I.78, L.84, V.87, Y.88, L.91, A.99, M.102, V.103, V.111, L.118, L.121, F.153 No protein-ligand interaction detected (PLIP)

2 x HED: 2-HYDROXYETHYL DISULFIDE(Non-covalent)

HED.5: 5 residues within 4Å: Chain A: V.75, Y.88, A.93, R.96, I.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.88 HED.6: 7 residues within 4Å: Chain A: G.30, H.31, L.32, D.70, A.73, A.74, F.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.70 Water bridges: A:D.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding. J.Mol.Biol. (2009)

Release Date

2008-11-11

Peptides

Lysozyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysozyme

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