MolNFT v1 · #101615 · protein

Crystal structure of an N-terminally truncated capsid protein mutant of orsay virus

4NWW: “Crystal structure of an N-terminally truncated capsid protein mutant of orsay virus”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.78). MolNFT v1 #101615 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4NWW
Type: protein
Length: 1,031 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: E9KNV5
Ligands: CA
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein	protein	341	11% helix, 42% strand	E9KNV5
B, C	Capsid protein	protein	345	14% helix, 41% strand	E9KNV5

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, B, C

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

Pockets

9 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	1039	0.78	0.80	96	empty
2	1090	0.72	0.76	73	empty
3	423	0.68	0.80	37	empty
4	350	0.67	0.81	42	empty
5	551	0.61	0.74	46	empty

Interfaces

3 interfaces between chains.

B–C · 1621 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1620 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1604 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4NWW · Crystal structure of an N-terminally truncated capsid protein mutant of Orsay virus · 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 E9KNV5
Elsewhere: RCSB PDB 4NWW · PDBe 4NWW · UniProt E9KNV5

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