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Crystal structure of HPV58/33/52 chimeric L1 pentamer

Analyse Crystal structure of HPV58/33/52 chimeric L1 pentamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IGC
Type: protein
Length: 16,652 residues
Chains: 40
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.5
Source: Human papillomavirus type 58
Molecule: Major capsid protein L1
UniProt: P26535
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · resolution 3.5 · 13 distinct chains · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major capsid protein L1	protein	420	15% helix, 39% strand	P26535
B	Major capsid protein L1	protein	413	15% helix, 40% strand	P26535
C	Major capsid protein L1	protein	416	15% helix, 39% strand	P26535
D	Major capsid protein L1	protein	416	15% helix, 40% strand	P26535
E	Major capsid protein L1	protein	414	14% helix, 38% strand	P26535
F, e	Major capsid protein L1	protein	416	15% helix, 40% strand	P26535
G, L, Q, V, a, f, k	Major capsid protein L1	protein	414	14% helix, 40% strand	P26535
H, M, R, W, b, g, l	Major capsid protein L1	protein	415	14% helix, 39% strand	P26535
I, S, X, c, h, m	Major capsid protein L1	protein	418	15% helix, 39% strand	P26535
J, O, T, Y, d, i, n	Major capsid protein L1	protein	420	15% helix, 39% strand	P26535
K, P, Z, j	Major capsid protein L1	protein	415	14% helix, 40% strand	P26535
N	Major capsid protein L1	protein	416	15% helix, 39% strand	P26535
U	Major capsid protein L1	protein	414	15% helix, 39% strand	P26535

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	1001	0.83	0.84	93	empty
2	796	0.80	0.83	87	empty
3	1072	0.78	0.80	114	empty
4	297	0.78	0.89	65	empty
5	939	0.76	0.79	83	empty

Interfaces

156 interfaces between chains.

W–X · 3927 Å² buried · 91 hydrogen bonds · protein-protein
a–d · 3784 Å² buried · 71 hydrogen bonds · protein-protein
e–g · 3728 Å² buried · 72 hydrogen bonds · protein-protein
X–Y · 3718 Å² buried · 61 hydrogen bonds · protein-protein
I–J · 3713 Å² buried · 63 hydrogen bonds · protein-protein

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 P26535
Elsewhere: RCSB PDB 6IGC · PDBe 6IGC · UniProt P26535

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