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Structure of the human srp S domain with SRP72 RNA-binding domain

Analyse Structure of the human srp S domain with SRP72 RNA-binding domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M73
Type: protein + RNA
Length: 984 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human gene for small cytoplasmic 7SL RNA (7L30.1); Signal recognition particle 19 kda…
UniProt: P09132, Q9UHB9, O76094
Ligands: MG, K
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 7 distinct chains · 56% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Human gene for small cytoplasmic 7SL RNA (7L30.1)	rna	145	—	—
B	Signal recognition particle 19 kda protein	protein	108	32% helix, 14% strand	P09132
C	Signal recognition particle subunit SRP68	protein	197	73% helix, 0% strand	Q9UHB9
D	Signal recognition particle subunit SRP72	protein	47	36% helix, 0% strand	O76094
F	Signal recognition particle 19 kda protein	protein	104	31% helix, 20% strand	P09132
G	Signal recognition particle subunit SRP68	protein	197	75% helix, 3% strand	Q9UHB9
H	Signal recognition particle subunit SRP72	protein	41	32% helix, 0% strand	O76094

Ligands and binding sites

MG · Magnesium ion · metal · 45 copies · chains A, D, C, E, G
K · Potassium ion · metal · 10 copies · chains A, D, E
GOL · Glycerol · additive · 9 copies · chains A, B, E

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1134	0.73	0.77	62	MG, K
2	848	0.72	0.78	44	GOL
3	856	0.72	0.78	64	MG, K, GOL
4	662	0.70	0.78	48	MG, GOL
5	843	0.68	0.75	57	MG, K, GOL

Interfaces

7 interfaces between chains.

A–C · 1616 Å² buried · 40 hydrogen bonds · protein-nucleic
E–G · 1541 Å² buried · 49 hydrogen bonds · protein-nucleic
A–B · 967 Å² buried · 37 hydrogen bonds · protein-nucleic
E–F · 915 Å² buried · 28 hydrogen bonds · protein-nucleic
A–D · 859 Å² buried · 25 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

5M73 · Structure of the human SRP S domain with SRP72 RNA-binding domain · the same entry in another collection · chain H against H, TM-score 1.00
Q9UHB9 · AlphaFold monomer V2.0 prediction for signal recognition particle subunit SRP68 (Q9UHB9) · a predicted model of the same protein · chain C against A, TM-score 0.98
P09132 · AlphaFold monomer V2.0 prediction for signal recognition particle 19 kda protein (P09132) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P09132
Every structure of UniProt Q9UHB9
Every structure of UniProt O76094
Elsewhere: RCSB PDB 5M73 · PDBe 5M73 · UniProt P09132 · UniProt Q9UHB9 · UniProt O76094

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