MolNFT v1 · #142735 · protein

Structure of seneca valley virus in neutral condition

6ADT · VP1: “Structure of seneca valley virus in neutral condition”. Electron microscopy, 12 pockets (best druggability 0.69). MolNFT v1 #142735 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ADT
Type: protein
Length: 788 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP3; VP2; VP4
Pockets: 12 · best druggability 0.69

Structure

electron microscopy · 4 distinct chains · 8% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	258	6% helix, 32% strand	—
C	VP3	protein	228	8% helix, 29% strand	—
B	VP2	protein	267	9% helix, 33% strand	—
D	VP4	protein	35	11% helix, 11% strand	—

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.69	0.88	25	empty
2	225	0.56	0.78	30	empty
3	168	0.51	0.78	28	empty
4	82	0.50	0.84	17	empty
5	118	0.46	0.78	24	empty

Interfaces

6 interfaces between chains.

A–C · 3348 Å² buried · 45 hydrogen bonds · protein-protein
A–B · 2787 Å² buried · 34 hydrogen bonds · protein-protein
C–B · 1681 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 923 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 532 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6ADT · Structure of Seneca Valley Virus in neutral condition · 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
Elsewhere: RCSB PDB 6ADT · PDBe 6ADT

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