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Crystal structure of HUMANPAPILLOMAVIRUS18 (HPV18) capsid L1 pentamers bound to heparin oligosaccharides

Analyse Crystal structure of HUMANPAPILLOMAVIRUS18 (HPV18) capsid L1 pentamers bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W1X
Type: protein
Length: 6,330 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein L1
UniProt: Q5G244
Ligands: JHM, IDS
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	Major capsid protein L1	protein	422	13% helix, 35% strand	Q5G244

Ligands and binding sites

JHM · 2-deoxy-6-O-sulfo-alpha-D-glucopyranose · ligand · 45 copies · chains A, E, D, B, C, F, J, G, H, K, L, O, M, N
IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 45 copies · chains A, E, C, B, D, F, J, G, H, K, L, O, M, N

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1070	0.74	0.77	99	empty
2	948	0.73	0.77	87	empty
3	804	0.71	0.77	55	empty
4	512	0.68	0.79	73	empty
5	262	0.66	0.83	46	empty

Interfaces

38 interfaces between chains.

C–D · 3795 Å² buried · 50 hydrogen bonds · protein-protein
L–M · 3754 Å² buried · 48 hydrogen bonds · protein-protein
G–H · 3723 Å² buried · 54 hydrogen bonds · protein-protein
N–O · 3701 Å² buried · 56 hydrogen bonds · protein-protein
A–B · 3688 Å² buried · 54 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan (glycosylation, O-glycosylation).

Compared structures

5W1X · Crystal Structure of Humanpapillomavirus18 (HPV18) Capsid L1 Pentamers Bound to Heparin… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q5G244
Elsewhere: RCSB PDB 5W1X · PDBe 5W1X · UniProt Q5G244

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