MolNFT v1 · #140395 · protein

Crystal structure of HPV59 pentamer in complex with the Fab fragment of antibody 28F10

5Y9F · Major capsid protein L1: “Crystal structure of HPV59 pentamer in complex with the Fab fragment of antibody 28F10”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #140395 on GenesisL1: 3D structure, binding sites…

PDB: 5Y9F
Type: protein
Length: 8,582 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein L1; Light chains of Fab fragment of antibody 28F10; Heavy chain of…
UniProt: Q81971
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 9 distinct chains · 8% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, G, H, I, J	Major capsid protein L1	protein	420	11% helix, 38% strand	Q81971
C, D, F	Major capsid protein L1	protein	421	11% helix, 38% strand	Q81971
E	Major capsid protein L1	protein	427	11% helix, 37% strand	Q81971
K, Q, M, Y, a, U	Light chains of Fab fragment of antibody 28F10	protein	217	6% helix, 52% strand	—
L	Heavy chain of Fab fragment of antibody 28F10	protein	222	4% helix, 48% strand	—
O, S, c	Light chains of Fab fragment of antibody 28F10	protein	218	6% helix, 51% strand	—
P, T, N, V, X, Z, b	Heavy chain of Fab fragment of antibody 28F10	protein	219	3% helix, 47% strand	—
R, d	Heavy chain of Fab fragment of antibody 28F10	protein	221	4% helix, 48% strand	—
W	Light chains of Fab fragment of antibody 28F10	protein	219	6% helix, 52% 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	866	0.75	0.79	83	empty
2	812	0.74	0.79	79	empty
3	1192	0.73	0.76	116	empty
4	522	0.71	0.81	67	empty
5	747	0.70	0.77	89	empty

Interfaces

76 interfaces between chains.

B–E · 3667 Å² buried · 67 hydrogen bonds · protein-protein
D–E · 3652 Å² buried · 63 hydrogen bonds · protein-protein
F–J · 3651 Å² buried · 64 hydrogen bonds · protein-protein
H–I · 3651 Å² buried · 58 hydrogen bonds · protein-protein
F–G · 3623 Å² buried · 67 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 41 disulfide (disulfide).

Compared structures

5Y9F · Crystal structure of HPV59 pentamer in complex with the Fab fragment of antibody 28F10 · the same entry in another collection · chain B against B, 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 Q81971
Elsewhere: RCSB PDB 5Y9F · PDBe 5Y9F · UniProt Q81971

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.