SMTL ID : 8gao.1

bacteriophage T4 stalled primosome with mutant gp41-E227Q

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

1 x GTP- C- C- G- A: RNA (5'-D(*(GTP))-R(P*CP*CP*GP*A)-3')(Non-covalent)

GTP-C-C-G-A.1: 15 residues within 4Å: Chain G: D.40, S.41, D.44, R.49, Y.64, N.65, A.201, Q.203, K.204, Y.205 Chain I: T.36, C.37, G.38, G.39, C.40 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:S.41, G:S.41, G:S.41, G:N.65 Salt bridges: G:R.49, G:R.49, G:R.49

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

AGS.2: 19 residues within 4Å: Chain A: K.405, R.407, Y.408, D.410 Chain B: V.199, N.200, V.201, G.202, K.203, S.204, L.205, Q.227, R.236, L.246, D.247, Y.312, K.423, Q.426 Ligands: MG.3 20 PLIP interactions: 5 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:K.405, A:R.407, A:D.410, A:D.410, B:N.200, B:N.200, B:N.200, B:V.201, B:G.202, B:K.203, B:S.204, B:L.205, B:R.236, B:D.247, B:D.250, B:K.423, B:Q.426 Salt bridges: A:K.405, B:K.203, B:R.236 AGS.4: 23 residues within 4Å: Chain B: P.378, A.379, K.405, S.406, R.407, Y.408, G.409, D.410 Chain C: V.199, N.200, V.201, G.202, K.203, S.204, L.205, Q.227, K.235, R.236, L.246, Q.355, K.423, Q.426 Ligands: MG.5 24 PLIP interactions: 18 interactions with chain C, 6 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:K.203, C:S.204, C:L.205, C:Q.227, C:Q.227, C:K.235, C:K.235, C:R.236, C:R.236, C:Q.426, B:K.405, B:R.407, B:D.410, B:D.410, B:K.411 Salt bridges: C:K.203, C:R.236, B:K.405 AGS.6: 23 residues within 4Å: Chain C: A.379, K.405, S.406, 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, Q.227, R.236, L.246, Q.355, K.423, Q.426 Ligands: MG.7 16 PLIP interactions: 12 interactions with chain D, 4 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:R.236, D:Q.355, D:K.423, C:R.407, C:D.410, C:D.410, C:K.411 Salt bridges: D:R.236 AGS.8: 19 residues within 4Å: Chain D: K.405, S.406, R.407, Y.408, G.409, D.410, K.411 Chain E: V.199, N.200, G.202, K.203, S.204, L.205, Q.227, R.236, L.246, Q.355, K.423 Ligands: MG.9 16 PLIP interactions: 5 interactions with chain D, 11 interactions with chain E Hydrogen bonds: D:S.406, D:R.407, D:R.407, D:D.410, D:K.411, E:N.200, E:G.202, E:K.203, E:K.203, E:S.204, E:L.205, E:Q.227, E:Q.355, E:K.423 Salt bridges: E:K.203, E:R.236 AGS.10: 20 residues within 4Å: Chain E: K.405, S.406, R.407, Y.408, G.409, D.410, K.411 Chain F: G.198, V.199, N.200, V.201, G.202, K.203, S.204, L.205, Q.227, R.236, L.246, K.423 Ligands: MG.11 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:N.200, F:N.200, F:V.201, F:G.202, F:K.203, F:S.204, F:L.205, F:Q.227, E:R.407, E:Y.408, E:K.411 Salt bridges: F:R.236

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain B: K.203, S.204, Q.227 Ligands: AGS.2 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: S.204, Q.227 Ligands: AGS.4 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain D: Q.227 Ligands: AGS.6 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain E: S.204, Q.227 Ligands: AGS.8 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain F: S.204, Q.227 Ligands: AGS.10 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain G: C.35, C.38, C.63, C.66 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.35, G:C.38, G:C.63, G:C.66

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

2023-06-07

Peptides

DnaB-like replicative helicase: ABCDEF
DNA primase: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

DnaB-like replicative helicase

DNA primase

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