SMTL ID : 4pk0.1

CRYSTAL STRUCTURE OF T4 LYSOZYME-PEPTIDE IN COMPLEX WITH TEICOPLANIN-A2-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x GHP- 3MY- 3FG- GHP- GHP- OMY- 3FG: TEICOPLANIN-A2-2(Non-covalent)

GHP-3MY-3FG-GHP-GHP-OMY-3FG.1: 16 residues within 4Å: Chain A: G.12, L.13, R.14, L.15, K.16, Y.18, K.60, P.168, A.169, A.170, A.171 Ligands: GCS.2, NAG.3, MAN.4, T55.5, PO4.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.14, A:L.15 Hydrogen bonds: A:L.13, A:L.13, A:L.15 Water bridges: A:R.14, A:R.14, A:R.14 pi-Stacking: A:Y.18

1 x GCS: 2-amino-2-deoxy-beta-D-glucopyranose(Non-covalent)

GCS.2: 7 residues within 4Å: Chain A: A.166, P.168, A.171 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, T55.5 No protein-ligand interaction detected (PLIP)

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

NAG.3: 7 residues within 4Å: Chain A: I.9, D.10, E.11, G.12, H.167, A.169 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.1 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.4: 6 residues within 4Å: Chain A: R.14 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, PO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.14, A:R.14

1 x T55: 8-METHYLNONANOIC ACID(Non-covalent)

T55.5: 8 residues within 4Å: Chain A: R.8, I.29, K.60, A.63, E.64 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GCS.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.63, A:E.64, A:E.64

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

CL.6: 2 residues within 4Å: Chain A: R.76, R.80 Ligand excluded by PLIP

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

NA.7: 2 residues within 4Å: Chain A: K.16 Ligands: PO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.16, A:K.16

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

PO4.8: 4 residues within 4Å: Chain A: K.16 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, MAN.4, NA.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.14 Salt bridges: A:K.16

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: E.22, Q.105, M.106, R.137, W.138, Q.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, S. et al., X-ray Crystal Structure of Teicoplanin A2-2 Bound to a Catalytic Peptide Sequence via the Carrier Protein Strategy. J.Org.Chem. (2014)

Release Date

2014-09-10

Peptides

Lysozyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysozyme