MolNFT v1 · #29598 · protein + RNA

Structure of bacteriophage coat protein-loop RNA complex

1ZDJ · Protein (MS2 protein capsid): “Structure of bacteriophage coat protein-loop RNA complex”. X-ray diffraction, 2 pockets (best druggability 0.77). MolNFT v1 #29598 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZDJ
Type: protein + RNA
Length: 403 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (MS2 protein capsid); RNA (5'-R(*GP*GP*AP*UP*CP*AP*CP*C)-3')
UniProt: P03612
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Protein (MS2 protein capsid)	protein	129	18% helix, 47% strand	P03612
R, S	RNA (5'-R(GPGPAPUPCPAPCPC)-3')	rna	8	—	—

Pockets

2 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	793	0.77	0.81	105	empty
2	212	0.47	0.75	30	empty

Interfaces

5 interfaces between chains.

B–C · 565 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 527 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 520 Å² buried · 7 hydrogen bonds · protein-protein
A–R · 364 Å² buried · 10 hydrogen bonds · protein-nucleic
C–S · 357 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

1ZDJ · Structure of bacteriophage coat protein-loop RNA complex · 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 P03612
Elsewhere: RCSB PDB 1ZDJ · PDBe 1ZDJ · UniProt P03612

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