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Crystal structure of the SRP19/S-domain srp RNA complex of sulfolobus solfataricus

Analyse Crystal structure of the SRP19/S-domain srp RNA complex of sulfolobus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KTW
Type: protein + RNA
Length: 376 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Signal recognition particle 19 kda protein; Srp RNA
UniProt: Q980W2
Ligands: MG, K
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Signal recognition particle 19 kda protein	protein	92	37% helix, 13% strand	Q980W2
B	Signal recognition particle 19 kda protein	protein	93	38% helix, 13% strand	Q980W2
C	Srp RNA	rna	96	—	—
D	Srp RNA	rna	95	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 6 copies · chains B, C, A, D
K · Potassium ion · metal · 4 copies · chains D, C

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

Pockets

10 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	970	0.74	0.78	72	K, MG
2	773	0.70	0.77	43	empty
3	635	0.68	0.78	35	empty
4	398	0.58	0.76	29	K, MG
5	123	0.42	0.77	13	empty

Interfaces

5 interfaces between chains.

B–D · 1340 Å² buried · 43 hydrogen bonds · protein-nucleic
A–C · 1338 Å² buried · 44 hydrogen bonds · protein-nucleic
C–D · 178 Å² buried · 3 hydrogen bonds · nucleic-nucleic
B–C · 177 Å² buried · 0 hydrogen bonds · protein-nucleic
A–D · 69 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

3KTW · Crystal structure of the SRP19/S-domain SRP RNA complex of Sulfolobus solfataricus · the same entry in another collection · chain A against A, TM-score 1.00
Q980W2 · AlphaFold monomer V2.0 prediction for signal recognition particle 19 kda protein (Q980W2) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 Q980W2
Elsewhere: RCSB PDB 3KTW · PDBe 3KTW · UniProt Q980W2

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