SMTL ID : 3dke.1

Polar and non-polar cavities in phage T4 lysozyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x K: POTASSIUM ION(Non-covalent)

K.1: 2 residues within 4Å: Chain A: E.11, Y.18 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.11, A:Y.18, H2O.1, H2O.2, H2O.3

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

CL.2: 4 residues within 4Å: Chain A: T.142, P.143, N.144, R.145 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: N.132, K.135 Ligand excluded by PLIP

1 x AZI: AZIDE ION(Non-covalent)

AZI.4: 1 residues within 4Å: Chain A: K.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.19 Water bridges: A:R.14, A:K.19, A:K.19

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 10 residues within 4Å: Chain A: M.106, G.110, V.111, A.112, G.113, F.114, S.136, R.137, W.138 Ligands: HED.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.113, A:R.137, A:W.138 Water bridges: A:A.112

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.6: 4 residues within 4Å: Chain A: T.34, S.36, A.41, E.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.34 Water bridges: A:L.33, A:K.35, A:E.45 BME.7: 3 residues within 4Å: Chain A: Q.69, D.72, A.73 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.69

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

HED.8: 6 residues within 4Å: Chain A: N.81, K.83, L.84, T.115, L.118, R.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.81, A:N.81, A:T.115 HED.9: 9 residues within 4Å: Chain A: E.22, Y.24, K.35, Q.105, M.106, T.109, R.137, W.138 Ligands: EPE.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.35, A:R.137

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: G.30, H.31, L.32, D.70, F.104, G.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.32, A:L.32 Water bridges: A:V.103 GOL.11: 3 residues within 4Å: Chain A: I.3, Y.88, I.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.88, A:A.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Use of experimental crystallographic phases to examine the hydration of polar and nonpolar cavities in T4 lysozyme. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2008-11-25

Peptides

Lysozyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

Lysozyme