SMTL ID : 1ocy.1

Structure of the receptor-binding domain of the bacteriophage T4 short tail fibre

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 6 residues within 4Å: Chain A: Y.125, D.126, D.127, R.136 Chain C: R.151 Ligands: SO4.2 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Y.125, A:D.127, A:R.136, A:R.136, C:R.151 Salt bridges: C:R.151, C:R.151 CIT.5: 6 residues within 4Å: Chain A: R.151 Chain B: Y.125, D.126, D.127, R.136 Ligands: SO4.6 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.125, B:D.127, B:R.136, B:R.136, A:R.151 Salt bridges: A:R.151, A:R.151 CIT.9: 6 residues within 4Å: Chain B: R.151 Chain C: Y.125, D.126, D.127, R.136 Ligands: SO4.10 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Y.125, C:D.127, C:R.136, C:R.136, B:R.151 Salt bridges: B:R.151, B:R.151

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

SO4.2: 5 residues within 4Å: Chain A: R.135, R.136 Chain B: Y.171 Chain C: R.151 Ligands: CIT.1 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:R.136, B:Y.171 Water bridges: A:R.135 Salt bridges: C:R.151 SO4.3: 2 residues within 4Å: Chain A: S.57, S.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.58 SO4.6: 5 residues within 4Å: Chain A: R.151 Chain B: R.135, R.136 Chain C: Y.171 Ligands: CIT.5 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:R.136, C:Y.171 Water bridges: B:R.135 Salt bridges: A:R.151 SO4.7: 2 residues within 4Å: Chain B: S.57, S.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.58 SO4.10: 5 residues within 4Å: Chain A: Y.171 Chain B: R.151 Chain C: R.135, R.136 Ligands: CIT.9 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:Y.171, C:R.136 Water bridges: C:R.135 Salt bridges: B:R.151 SO4.11: 2 residues within 4Å: Chain C: S.57, S.58 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.58

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 8 residues within 4Å: Chain A: H.116, H.118 Chain B: H.116, H.118 Chain C: H.116, H.118 Ligands: ZN.8, ZN.12 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Metal complexes: C:H.116, C:H.118, A:H.116, A:H.118, B:H.116, B:H.118 ZN.8: 8 residues within 4Å: Chain A: H.116, H.118 Chain B: H.116, H.118 Chain C: H.116, H.118 Ligands: ZN.4, ZN.12 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Metal complexes: C:H.116, C:H.118, A:H.116, A:H.118, B:H.116, B:H.118 ZN.12: 8 residues within 4Å: Chain A: H.116, H.118 Chain B: H.116, H.118 Chain C: H.116, H.118 Ligands: ZN.4, ZN.8 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Metal complexes: C:H.116, C:H.118, A:H.116, A:H.118, B:H.116, B:H.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomassen, E. et al., The Structure of the Receptor-Binding Domain of the Bacteriophage T4 Short Tail Fibre Reveals a Knitted Trimeric Metal-Binding Fold. J.Mol.Biol. (2003)

Release Date

2003-07-24

Peptides

BACTERIOPHAGE T4 SHORT TAIL FIBRE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

BACTERIOPHAGE T4 SHORT TAIL FIBRE