MolNFT v1 · #141134 · protein

Crystal structure of the C-terminal fragment of NS1 protein from yellow fever virus

5YXA · Non-structural protein 1: “Crystal structure of the C-terminal fragment of NS1 protein from yellow fever virus”. X-ray diffraction, 6 pockets (best druggability 0.74). MolNFT v1 #141134 on GenesisL1: 3D structure, binding sites and…

PDB: 5YXA
Type: protein
Length: 708 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Non-structural protein 1
UniProt: A0A161I252
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Non-structural protein 1	protein	177	7% helix, 33% strand	A0A161I252

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1093	0.74	0.77	98	empty
2	970	0.73	0.77	106	empty
3	110	0.39	0.75	18	empty
4	89	0.38	0.76	19	empty
5	59	0.32	0.76	20	empty

Interfaces

5 interfaces between chains.

A–B · 344 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 302 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 275 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 258 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 78 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5YXA · Crystal structure of the C-terminal fragment of NS1 protein from yellow fever virus · 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 A0A161I252
Elsewhere: RCSB PDB 5YXA · PDBe 5YXA · UniProt A0A161I252

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