MolNFT v1 · #182490 · protein + RNA

MS2 protein CAPSID/RNA complex

7MSF: “MS2 protein CAPSID/RNA complex”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #182490 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7MSF
Type: protein + RNA
Length: 412 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MS2 protein capsid; 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)- 3'
UniProt: P03612
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	MS2 protein capsid	protein	129	19% helix, 47% strand	P03612
R	5'-R(UPCPGPCPCPAPAPCPAPGPGPCPGPG)- 3'	rna	14	—	—
S	5'-R(UPCPGPCPCPAPAPCPAPGPGPCPGPG)- 3'	rna	11	—	—

Pockets

6 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	702	0.76	0.81	96	empty
2	219	0.59	0.80	31	empty
3	197	0.42	0.73	20	empty
4	129	0.40	0.75	23	empty
5	75	0.32	0.74	17	empty

Interfaces

5 interfaces between chains.

B–C · 548 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 544 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 512 Å² buried · 6 hydrogen bonds · protein-protein
A–R · 416 Å² buried · 13 hydrogen bonds · protein-nucleic
C–S · 361 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

7MSF · MS2 protein CAPSID/RNA complex · the same entry in another collection · chain R against R, 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 P03612
Elsewhere: RCSB PDB 7MSF · PDBe 7MSF · UniProt P03612

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