MolNFT v1 · #168203 · protein

Co-crystal structures of chikv NSP3 macrodomain with pyrimidone fragments

6W8M · Nonstructural polyprotein: “Co-crystal structures of chikv NSP3 macrodomain with pyrimidone fragments”. X-ray diffraction, 1 ligand (TJY), 8 pockets (best druggability 0.67). MolNFT v1 #168203 on GenesisL1: 3D structure, binding…

PDB: 6W8M
Type: protein
Length: 642 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nonstructural polyprotein
UniProt: A0A4D6GPC4
Ligands: TJY
Pockets: 8 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Nonstructural polyprotein	protein	160	39% helix, 20% strand	A0A4D6GPC4
B	Nonstructural polyprotein	protein	162	39% helix, 20% strand	A0A4D6GPC4

Ligands and binding sites

TJY · 2-oxo-1,2-dihydroquinazoline-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	477	0.67	0.78	57	TJY
2	294	0.63	0.80	38	TJY
3	449	0.62	0.76	64	empty
4	223	0.59	0.80	28	TJY
5	196	0.59	0.81	29	TJY

Interfaces

4 interfaces between chains.

C–D · 594 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 448 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 348 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 235 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6W8M · Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments · 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 A0A4D6GPC4
Elsewhere: RCSB PDB 6W8M · PDBe 6W8M · UniProt A0A4D6GPC4

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