SMTL ID : 6ibg.1

Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-12-mer

Ligands

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 9 residues within 4Å: Chain A: R.78, G.331, V.334, Q.338, E.379, E.380, R.381, N.382 Chain I: R.381 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain A Hydrogen bonds: I:R.381 Hydrophobic interactions: A:V.334, A:Q.338 Water bridges: A:R.78 MPD.2: 10 residues within 4Å: Chain A: R.381 Chain B: R.78, G.331, V.334, S.335, Q.338, E.379, E.380, R.381, N.382 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:R.381, B:R.78 Hydrophobic interactions: B:V.334, B:Q.338 MPD.3: 6 residues within 4Å: Chain B: R.381 Chain C: R.78, G.331, E.379, E.380, R.381 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.381 Water bridges: C:R.78, C:E.379 MPD.4: 9 residues within 4Å: Chain D: R.78, G.331, V.334, Q.338, E.379, E.380, R.381, N.382 Chain L: R.381 4 PLIP interactions: 1 interactions with chain L, 3 interactions with chain D Hydrogen bonds: L:R.381 Hydrophobic interactions: D:V.334, D:Q.338 Water bridges: D:R.78 MPD.5: 10 residues within 4Å: Chain D: R.381 Chain E: R.78, G.331, V.334, S.335, Q.338, E.379, E.380, R.381, N.382 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Water bridges: D:R.381, E:R.78 Hydrophobic interactions: E:V.334, E:Q.338 MPD.6: 6 residues within 4Å: Chain E: R.381 Chain F: R.78, G.331, E.379, E.380, R.381 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Water bridges: F:R.78, F:E.379 Hydrogen bonds: E:R.381 MPD.7: 9 residues within 4Å: Chain F: R.381 Chain G: R.78, G.331, V.334, Q.338, E.379, E.380, R.381, N.382 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:V.334, G:Q.338 Water bridges: G:R.78 Hydrogen bonds: F:R.381 MPD.8: 10 residues within 4Å: Chain G: R.381 Chain H: R.78, G.331, V.334, S.335, Q.338, E.379, E.380, R.381, N.382 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain H Water bridges: G:R.381, H:R.78 Hydrophobic interactions: H:V.334, H:Q.338 MPD.9: 6 residues within 4Å: Chain H: R.381 Chain I: R.78, G.331, E.379, E.380, R.381 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain H Water bridges: I:R.78, I:E.379 Hydrogen bonds: H:R.381 MPD.10: 9 residues within 4Å: Chain C: R.381 Chain J: R.78, G.331, V.334, Q.338, E.379, E.380, R.381, N.382 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain C Hydrophobic interactions: J:V.334, J:Q.338 Water bridges: J:R.78 Hydrogen bonds: C:R.381 MPD.11: 10 residues within 4Å: Chain J: R.381 Chain K: R.78, G.331, V.334, S.335, Q.338, E.379, E.380, R.381, N.382 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain K Water bridges: J:R.381, K:R.78 Hydrophobic interactions: K:V.334, K:Q.338 MPD.12: 6 residues within 4Å: Chain K: R.381 Chain L: R.78, G.331, E.379, E.380, R.381 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain K Water bridges: L:R.78, L:E.379 Hydrogen bonds: K:R.381

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bayfield, O.W. et al., Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2019-01-23

Peptides

Portal protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

Portal protein