SMTL ID : 5muv.1

Atomic structure fitted into a localized reconstruction of bacteriophage phi6 packaging hexamer P4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: S.133, E.150 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.133 CA.3: 5 residues within 4Å: Chain B: S.133, E.150, E.153, D.187 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.133 CA.6: 4 residues within 4Å: Chain C: S.133, E.150, E.153 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.133 CA.7: 4 residues within 4Å: Chain D: S.133, E.150, E.153 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.133 CA.9: 4 residues within 4Å: Chain E: S.133, E.150, E.153 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.133 CA.11: 4 residues within 4Å: Chain F: S.133, E.150, E.153 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.133

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 13 residues within 4Å: Chain A: A.127, G.129, S.130, G.131, K.132, S.133, I.134, E.153, G.260 Chain F: R.264, R.273, F.275 Ligands: CA.1 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain F Hydrogen bonds: A:G.129, A:S.130, A:G.131, A:K.132, A:S.133, A:I.134, F:R.264, F:R.273 Salt bridges: A:K.132, F:R.273 pi-Stacking: F:F.275, F:F.275 ADP.4: 13 residues within 4Å: Chain A: R.264, R.273, F.275 Chain B: A.127, G.129, S.130, G.131, K.132, S.133, I.134, E.153, G.260 Ligands: CA.3 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.129, B:S.130, B:G.131, B:K.132, B:S.133, B:I.134, A:R.264, A:R.273 Salt bridges: B:K.132, A:R.273 pi-Stacking: A:F.275, A:F.275 ADP.5: 14 residues within 4Å: Chain B: R.264, R.273, F.275 Chain C: A.127, T.128, G.129, S.130, G.131, K.132, S.133, I.134, E.153, G.260 Ligands: CA.6 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:R.264, B:R.273, C:G.129, C:S.130, C:G.131, C:K.132, C:S.133, C:I.134 Salt bridges: B:R.273, C:K.132 pi-Stacking: B:F.275 ADP.8: 13 residues within 4Å: Chain C: R.264, R.273, F.275 Chain D: A.127, G.129, S.130, G.131, K.132, S.133, I.134, E.153, G.260 Ligands: CA.7 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:G.129, D:S.130, D:G.131, D:K.132, D:S.133, D:I.134, C:R.264, C:R.273 Salt bridges: D:K.132, C:R.273 pi-Stacking: C:F.275, C:F.275 ADP.10: 13 residues within 4Å: Chain D: R.264, R.273, F.275 Chain E: A.127, G.129, S.130, G.131, K.132, S.133, I.134, E.153, G.260 Ligands: CA.9 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:G.129, E:S.130, E:G.131, E:K.132, E:S.133, E:S.133, E:I.134, D:R.264, D:R.273 Salt bridges: E:K.132 pi-Stacking: D:F.275 ADP.12: 13 residues within 4Å: Chain E: R.264, R.273, F.275 Chain F: A.127, G.129, S.130, G.131, K.132, S.133, I.134, E.153, G.260 Ligands: CA.11 12 PLIP interactions: 7 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:G.129, F:S.130, F:G.131, F:K.132, F:S.133, F:I.134, E:R.264, E:R.273 Salt bridges: F:K.132, E:R.273 pi-Stacking: E:F.275, E:F.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Z. et al., Double-stranded RNA virus outer shell assembly by bona fide domain-swapping. Nat Commun (2017)

Release Date

2017-03-22

Peptides

Packaging enzyme P4: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
I

D
J

E
K

F
L

Packaging enzyme P4

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