SMTL ID : 8due.1

Open state of T4 bacteriophage gp41 hexamer bound with single strand DNA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

AGS.1: 20 residues within 4Å: Chain A: K.405, R.407, Y.408, G.409, D.410 Chain B: G.198, V.199, N.200, V.201, G.202, K.203, S.204, L.205, E.227, R.236, L.246, Y.312, K.423, Q.426 Ligands: MG.2 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.200, B:N.200, B:V.201, B:G.202, B:K.203, B:S.204, B:S.204, B:L.205, B:R.236, B:R.236, B:K.423, B:Q.426, A:Y.408, A:D.410 Salt bridges: B:R.236 AGS.3: 23 residues within 4Å: Chain B: A.379, K.405, S.406, R.407, Y.408, G.409, D.410, K.411 Chain C: V.199, N.200, V.201, G.202, K.203, S.204, L.205, E.227, M.228, R.236, L.246, Y.312, Q.355, K.423 Ligands: MG.4 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:N.200, C:N.200, C:N.200, C:V.201, C:G.202, C:K.203, C:S.204, C:L.205, C:E.227, C:K.423, C:K.423, B:K.405, B:R.407, B:D.410, B:K.411 Salt bridges: C:K.203, C:R.236 AGS.5: 21 residues within 4Å: Chain C: K.405, R.407, Y.408, G.409, D.410, K.411 Chain D: G.198, V.199, N.200, V.201, G.202, K.203, S.204, L.205, E.227, R.236, L.246, D.247, K.423, Q.426 Ligands: MG.6 19 PLIP interactions: 13 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:N.200, D:N.200, D:N.200, D:V.201, D:G.202, D:K.203, D:S.204, D:L.205, D:E.227, D:R.236, D:Q.426, C:K.405, C:R.407, C:R.407, C:D.410, C:K.411 Salt bridges: D:K.203, D:R.236, C:K.405 AGS.7: 20 residues within 4Å: Chain D: K.405, R.407, Y.408, G.409, D.410, K.411 Chain E: V.199, N.200, V.201, G.202, K.203, S.204, L.205, E.227, M.228, R.236, L.246, K.423, Q.426 Ligands: MG.8 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:N.200, E:N.200, E:N.200, E:V.201, E:G.202, E:K.203, E:S.204, E:L.205, D:R.407, D:D.410, D:K.411 Salt bridges: E:R.236 AGS.9: 15 residues within 4Å: Chain E: K.405, R.407, Y.408, G.409, D.410 Chain F: V.199, N.200, V.201, G.202, K.203, S.204, R.236, L.246, K.423 Ligands: MG.10 13 PLIP interactions: 3 interactions with chain E, 10 interactions with chain F Hydrogen bonds: E:K.405, E:R.407, E:D.410, F:N.200, F:N.200, F:N.200, F:V.201, F:G.202, F:K.203, F:S.204, F:R.236 Salt bridges: F:K.203, F:R.236

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: G.202, S.204, E.227 Ligands: AGS.1 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.204, B:E.227, B:E.227 MG.4: 4 residues within 4Å: Chain C: S.204, M.228, R.236 Ligands: AGS.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain D: S.204, E.227 Ligands: AGS.5 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain E: S.204, E.227, M.228 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.227 MG.10: 2 residues within 4Å: Chain F: S.204 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, X. et al., Structural basis of the T4 bacteriophage primosome assembly and primer synthesis. Nat Commun (2023)

Release Date

2023-06-14

Peptides

DnaB-like replicative helicase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DnaB-like replicative helicase