SMTL ID : 7nxq.1 (1 other biounit)

Structure of the pentameric C-terminal domain of the capsid protein from Kaposi's sarcoma-associated herpesvirus (KSHV)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-pentamer

Ligands

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: S.42, G.44, I.48, R.265, L.425 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.48, A:L.425 Hydrogen bonds: A:G.44 Water bridges: A:R.265 Salt bridges: A:R.265 ACT.2: 5 residues within 4Å: Chain A: T.8, H.17, H.301, P.305 Chain B: Q.337 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.305 Salt bridges: A:H.17, A:H.301 Hydrogen bonds: B:Q.337 ACT.3: 5 residues within 4Å: Chain B: S.42, G.44, I.48, R.265, L.425 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.48, B:L.425 Hydrogen bonds: B:G.44 Salt bridges: B:R.265 ACT.4: 5 residues within 4Å: Chain B: T.8, H.17, H.301, P.305 Chain D: Q.337 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:Q.337 Hydrophobic interactions: B:P.305 Salt bridges: B:H.17, B:H.301 ACT.5: 5 residues within 4Å: Chain C: S.42, G.44, I.48, R.265, L.425 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.48, C:L.425 Hydrogen bonds: C:S.42, C:G.44 Salt bridges: C:R.265 ACT.6: 5 residues within 4Å: Chain A: Q.337 Chain C: T.8, H.17, H.301, P.305 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:P.305 Salt bridges: C:H.17, C:H.301 Hydrogen bonds: A:Q.337 ACT.7: 5 residues within 4Å: Chain D: S.42, G.44, I.48, R.265, L.425 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.48, D:L.425 Hydrogen bonds: D:S.42, D:G.44 Salt bridges: D:R.265 ACT.8: 4 residues within 4Å: Chain D: T.8, H.17, H.301, P.305 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.305 Hydrogen bonds: D:T.8 Salt bridges: D:H.17, D:H.301 ACT.9: 4 residues within 4Å: Chain E: S.42, G.44, I.48, R.265 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.48 Hydrogen bonds: E:S.42, E:G.44 Salt bridges: E:R.265 ACT.10: 5 residues within 4Å: Chain C: Q.337 Chain E: T.8, H.17, H.301, P.305 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain E Hydrogen bonds: C:Q.337, E:T.8 Hydrophobic interactions: E:P.305 Salt bridges: E:H.17, E:H.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naniima, P. et al., Assembly of infectious Kaposi's sarcoma-associated herpesvirus progeny requires formation of a pORF19 pentamer. Plos Biol. (2021)

Release Date

2021-10-13

Peptides

Capsid vertex component 2: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

D
H

E
J

Capsid vertex component 2

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