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Crystal structure of human papillomavirus type 52 pentamer

Analyse Crystal structure of human papillomavirus type 52 pentamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IGF
Type: protein
Length: 4,188 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein L1
UniProt: Q05138
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 10 distinct chains · 15% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major capsid protein L1	protein	413	15% helix, 39% strand	Q05138
B	Major capsid protein L1	protein	421	14% helix, 38% strand	Q05138
C	Major capsid protein L1	protein	427	14% helix, 37% strand	Q05138
D	Major capsid protein L1	protein	414	15% helix, 38% strand	Q05138
E	Major capsid protein L1	protein	429	14% helix, 38% strand	Q05138
F	Major capsid protein L1	protein	417	15% helix, 38% strand	Q05138
G	Major capsid protein L1	protein	418	14% helix, 38% strand	Q05138
H	Major capsid protein L1	protein	416	15% helix, 39% strand	Q05138
I	Major capsid protein L1	protein	416	14% helix, 38% strand	Q05138
J	Major capsid protein L1	protein	417	15% helix, 39% strand	Q05138

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	640	0.82	0.87	66	empty
2	743	0.71	0.78	94	empty
3	1187	0.69	0.74	81	empty
4	707	0.69	0.77	47	empty
5	176	0.67	0.87	27	empty

Interfaces

29 interfaces between chains.

G–J · 3569 Å² buried · 57 hydrogen bonds · protein-protein
A–B · 3519 Å² buried · 55 hydrogen bonds · protein-protein
D–E · 3515 Å² buried · 55 hydrogen bonds · protein-protein
I–J · 3500 Å² buried · 51 hydrogen bonds · protein-protein
F–G · 3493 Å² buried · 55 hydrogen bonds · protein-protein

Compared structures

6IGF · Crystal structure of Human Papillomavirus type 52 pentamer · 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 Q05138
Elsewhere: RCSB PDB 6IGF · PDBe 6IGF · UniProt Q05138

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