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Crystal structure of human papillomavirus type 33 pentamer

Analyse Crystal structure of human papillomavirus type 33 pentamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IGE
Type: protein
Length: 4,162 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein L1
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 10 distinct chains · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major capsid protein L1	protein	417	15% helix, 39% strand	—
B	Major capsid protein L1	protein	413	15% helix, 39% strand	—
C	Major capsid protein L1	protein	412	15% helix, 40% strand	—
D	Major capsid protein L1	protein	416	15% helix, 39% strand	—
E	Major capsid protein L1	protein	425	14% helix, 39% strand	—
F	Major capsid protein L1	protein	415	15% helix, 40% strand	—
G	Major capsid protein L1	protein	417	16% helix, 39% strand	—
H	Major capsid protein L1	protein	416	16% helix, 40% strand	—
I	Major capsid protein L1	protein	419	15% helix, 38% strand	—
J	Major capsid protein L1	protein	412	15% helix, 40% strand	—

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	1025	0.82	0.83	115	empty
2	1086	0.72	0.76	66	empty
3	1024	0.69	0.74	54	empty
4	1115	0.69	0.74	66	empty
5	450	0.68	0.79	76	empty

Interfaces

30 interfaces between chains.

I–J · 3661 Å² buried · 54 hydrogen bonds · protein-protein
F–G · 3652 Å² buried · 59 hydrogen bonds · protein-protein
D–E · 3591 Å² buried · 61 hydrogen bonds · protein-protein
A–C · 3565 Å² buried · 59 hydrogen bonds · protein-protein
F–H · 3559 Å² buried · 58 hydrogen bonds · protein-protein

Compared structures

6IGE · Crystal structure of Human Papillomavirus type 33 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
Elsewhere: RCSB PDB 6IGE · PDBe 6IGE

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