MolNFT v1 · #142654 · protein

Cryo-EM structure of T=3 penaeus vannamei nodavirus

6AB6 · Capsid protein: “Cryo-EM structure of T=3 penaeus vannamei nodavirus”. Electron microscopy, 1 ligand (CA), 4 pockets (best druggability 0.75). MolNFT v1 #142654 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6AB6
Type: protein
Length: 943 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: A5H7Q8
Ligands: CA
Pockets: 4 · best druggability 0.75

Structure

electron microscopy · 2 distinct chains · 7% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Capsid protein	protein	303	7% helix, 41% strand	A5H7Q8
C	Capsid protein	protein	337	7% helix, 37% strand	A5H7Q8

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, B, C

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

Pockets

4 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	79	0.75	0.98	22	empty
2	343	0.55	0.74	49	empty
3	79	0.35	0.76	21	empty
4	72	0.32	0.75	18	empty

Interfaces

3 interfaces between chains.

B–C · 1765 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 1029 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 974 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

6AB6 · Cryo-EM structure of T=3 Penaeus vannamei nodavirus · 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 A5H7Q8
Elsewhere: RCSB PDB 6AB6 · PDBe 6AB6 · UniProt A5H7Q8

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