SMTL ID : 6psk.1

Crystal structure of the complex between periplasmic domains of antiholin RI and holin T from T4 phage, in P6522

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.86, K.87, K.88 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.86, A:K.87 Salt bridges: A:K.87, A:K.88 SO4.2: 5 residues within 4Å: Chain A: S.77, N.78, S.79, K.80 Ligands: BTB.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.78, A:S.79 Salt bridges: A:K.80 SO4.7: 3 residues within 4Å: Chain B: T.86, K.87, K.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.87 Salt bridges: B:K.87, B:K.88 SO4.8: 5 residues within 4Å: Chain B: S.77, N.78, S.79, K.80 Ligands: BTB.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.78, B:S.79 Salt bridges: B:K.80 SO4.13: 3 residues within 4Å: Chain C: R.16, H.17, I.53 3 PLIP interactions: 3 interactions with chain C Water bridges: C:H.17 Salt bridges: C:R.16, C:H.17 SO4.16: 3 residues within 4Å: Chain D: R.16, H.17, I.53 3 PLIP interactions: 3 interactions with chain D Water bridges: D:H.17 Salt bridges: D:R.16, D:H.17

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.3: 5 residues within 4Å: Chain A: D.64, V.68, Y.75, Y.76 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.76 Water bridges: A:Y.75, A:K.80 BTB.9: 5 residues within 4Å: Chain B: D.64, V.68, Y.75, Y.76 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.76 Water bridges: B:K.80

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: K.30, K.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.143 EDO.5: 6 residues within 4Å: Chain A: E.18, R.118, D.120, H.121, I.122 Chain C: R.65 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.18, A:E.18, A:R.118, A:H.121, C:R.65 Water bridges: A:I.122 EDO.10: 2 residues within 4Å: Chain B: K.30, K.143 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.143 EDO.11: 6 residues within 4Å: Chain B: E.18, R.118, D.120, H.121, I.122 Chain D: R.65 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:R.65, B:E.18, B:R.118, B:H.121 Water bridges: B:I.122 EDO.14: 3 residues within 4Å: Chain C: H.6, S.47, D.49 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.49 Water bridges: C:K.9, B:N.71 EDO.15: 4 residues within 4Å: Chain C: N.24, N.68, I.69, K.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.68, C:K.70 EDO.17: 3 residues within 4Å: Chain D: H.6, S.47, D.49 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Water bridges: A:N.71, D:K.9 Hydrogen bonds: D:D.49 EDO.18: 4 residues within 4Å: Chain D: N.24, N.68, I.69, K.70 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.68, D:K.70

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

CL.6: 6 residues within 4Å: Chain A: Q.133, R.136, R.140 Chain B: R.136, R.140 Ligands: CL.12 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: R.136, R.140 Chain B: Q.133, R.136, R.140 Ligands: CL.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krieger, I.V. et al., The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition. J.Mol.Biol. (2020)

Release Date

2020-06-24

Peptides

Holin: AB
Antiholin: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
T

B
T

C
R

D
R

Holin

Antiholin

Related Entries With Identical Sequence