SMTL ID : 7jqq.1

The bacteriophage Phi-29 viral genome packaging motor assembly

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

3 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)(Covalent)

AGS.1: 16 residues within 4Å: Chain A: F.6, Y.7, A.25, R.26, G.27, I.28, G.29, K.30, S.31, Y.32, K.35, D.68, E.72, D.118 Chain B: K.105 Ligands: MG.2 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.7, A:G.27, A:G.29, A:K.30, A:K.30, A:S.31, A:S.31, A:Y.32, A:D.68, A:E.72, B:K.105, B:K.105 Salt bridges: A:K.30, A:K.35 pi-Stacking: A:F.6, A:Y.32, A:Y.32 AGS.3: 19 residues within 4Å: Chain B: F.6, G.24, A.25, R.26, G.27, I.28, G.29, K.30, S.31, Y.32, A.33, V.36, E.72, D.118, L.156, N.158 Chain C: K.105, R.146 Ligands: MG.4 16 PLIP interactions: 2 interactions with chain C, 14 interactions with chain B Hydrogen bonds: C:K.105, C:R.146, B:G.24, B:A.25, B:G.27, B:I.28, B:G.29, B:K.30, B:S.31, B:S.31, B:Y.32, B:E.72, B:D.118 Salt bridges: B:R.26, B:R.26 pi-Stacking: B:Y.32 AGS.5: 16 residues within 4Å: Chain C: F.6, A.25, R.26, G.27, I.28, G.29, K.30, S.31, Y.32, D.118, L.156 Chain D: K.105, S.106, A.108, R.146 Ligands: MG.6 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:R.26, C:G.27, C:I.28, C:G.29, C:K.30, C:S.31, C:S.31, C:Y.32, D:K.105, D:S.106, D:S.106, D:S.106, D:R.146 Salt bridges: C:K.30, C:K.35

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.31, D.118 Ligands: AGS.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.31, A:D.118, A:D.118 MG.4: 4 residues within 4Å: Chain B: S.31, D.118, L.156 Ligands: AGS.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.31, B:D.118, B:D.118 MG.6: 5 residues within 4Å: Chain C: S.31, D.118, L.156 Chain D: S.106 Ligands: AGS.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.31, C:D.118, C:D.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woodson, M. et al., A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA. Sci Adv (2021)

Release Date

2021-05-19

Peptides

DNA packaging protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

DNA packaging protein