MolNFT v1 · #18176 · protein + RNA

Bean pod mottle virus (bpmv), middle component

1PGL · 5'-R(*AP*GP*UP*CP*UP*C)-3': “Bean pod mottle virus (bpmv), middle component”. X-ray diffraction, 6 pockets (best druggability 0.65). MolNFT v1 #18176 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PGL
Type: protein + RNA
Length: 561 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*AP*GP*UP*CP*UP*C)-3'; Bean pod mottle virus small (S) subunit; Bean pod mottle…
UniProt: P23009
Pockets: 6 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
3	5'-R(APGPUPCPUPC)-3'	rna	6	—	—
1	Bean pod mottle virus small (S) subunit	protein	185	6% helix, 46% strand	P23009
2	Bean pod mottle virus large (L) subunit	protein	370	10% helix, 41% strand	P23009

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	129	0.65	0.88	30	empty
2	102	0.49	0.81	24	empty
3	161	0.46	0.76	22	empty
4	68	0.35	0.77	22	empty
5	69	0.33	0.75	17	empty

Interfaces

2 interfaces between chains.

1–2 · 2040 Å² buried · 29 hydrogen bonds · protein-protein
3–2 · 358 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

1PGL · Bean pod mottle virus (bpmv), middle component · the same entry in another collection · chain 3 against 3, 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 P23009
Elsewhere: RCSB PDB 1PGL · PDBe 1PGL · UniProt P23009

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