Structure of PDB 5y9e Chain D Binding Site BS01

Receptor Information

>5y9e Chain D (length=418) Species: 10598 (human papillomavirus 58)

KVVSTDEYVSRTSIYYYAGSSRLLAVGNPYFSIKSPNNNKKVLVPKVSGL
QYRVFRVRLPDPNKFGFPDTSFYNPDTQRLVWACVGLEIGRGQPLGVGVS
GHPYLNKFDDTETSNRYPAQPGSDNRECLSMDYKQTQLCLIGCKPPTGEH
WGKGVASNAAATDCPPLELFNSIIEDGDMVDTGFGCMDFGTLQANKSDVP
IDICNSTCKYPDYLKMASEPYGDSLFFFLRREQMFVRHFFNRAGKLGEAV
PDDLYIKGSGNTAVIQSSAFFPTPSGSIVTSESQLFNKPYWLQRAQGHNN
GICWGNQLFVTVVDTTRSTNMTLCTEVTKEGTYKNDNFKEYVRHVEEYDL
QFVFQLCKITLTAEIMTYIHTMDSNILEDWQFDPLNKYTFWEVNLKEKFS
ADLDQFPLGRKFLLQSGL

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 5y9e Chain C Residue 508

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5y9e Crystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus.
• Resolution: 2.042 Å
• Binding residue (original residue number in PDB): R41 E368
• Binding residue (residue number reindexed from 1): R22 E347
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005198 structural molecule activity

Biological Process

• GO:0019062 virion attachment to host cell
• GO:0046718 symbiont entry into host cell
• GO:0075509 endocytosis involved in viral entry into host cell

Cellular Component

• GO:0019028 viral capsid
• GO:0039620 T=7 icosahedral viral capsid
• GO:0042025 host cell nucleus

External links

• PDB: RCSB:5y9e, PDBe:5y9e, PDBj:5y9e
• PDBsum: 5y9e
• PubMed: 28951471
• UniProt: P26535|VL1_HPV58 Major capsid protein L1 (Gene Name=L1)