SMTL ID : 2dqa.1

Crystal Structure of Tapes japonica Lysozyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 15 residues within 4Å: Chain A: Q.41, I.42, K.43, P.45, Y.46, D.49, Y.74, Y.78, Y.82, H.95, N.96, G.97, G.98, P.99 Ligands: PT.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.45 Hydrogen bonds: A:D.49, A:Y.78, A:Y.82 Water bridges: A:Y.82 NAG-NAG-NAG.2: 17 residues within 4Å: Chain A: K.109 Chain B: Q.41, I.42, K.43, P.45, Y.46, D.49, Y.74, Y.78, Y.82, H.95, N.96, G.97, G.98, P.99 Ligands: PT.4, PT.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.45 Hydrogen bonds: B:D.49, B:Y.78, B:Y.82 Water bridges: B:R.77, B:R.77

8 x PT: PLATINUM (II) ION(Non-covalent)(Non-functional Binders)

PT.3: 2 residues within 4Å: Chain A: M.30 Ligands: PT.5 No protein-ligand interaction detected (PLIP) PT.4: 2 residues within 4Å: Chain A: K.109 Ligands: NAG-NAG-NAG.2 No protein-ligand interaction detected (PLIP) PT.5: 2 residues within 4Å: Chain A: M.30 Ligands: PT.3 No protein-ligand interaction detected (PLIP) PT.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PT.7: 1 residues within 4Å: Ligands: NAG-NAG-NAG.1 No protein-ligand interaction detected (PLIP) PT.10: 1 residues within 4Å: Chain B: M.30 No protein-ligand interaction detected (PLIP) PT.11: 2 residues within 4Å: Ligands: NAG-NAG-NAG.2, PT.12 No protein-ligand interaction detected (PLIP) PT.12: 1 residues within 4Å: Ligands: PT.11 No protein-ligand interaction detected (PLIP)

2 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.8: 5 residues within 4Å: Chain B: M.6, S.8, L.86, N.87, K.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.86 Water bridges: B:M.6, B:S.8 BGC.9: 4 residues within 4Å: Chain B: R.83, C.84, P.85, L.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.86 Water bridges: B:R.83, B:L.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto, T. et al., Crystal Structure of Tapes japonica Lysozyme with Substrate Analogue: STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND MANIFESTATION OF ITS CHITINASE ACTIVITY ACCOMPANIED BY QUATERNARY STRUCTURAL CHANGE. J.Biol.Chem. (2007)

Release Date

2007-06-12

Peptides

Lysozyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysozyme