Research workbench

Srp-sr at the distal site conformation

Analyse Srp-sr at the distal site conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OBQ
Type: protein + RNA
Length: 1,840 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Srp RNA; Signal recognition particle 19; EM14S01-3B_G0054400.MRNA.1.CDS.1; Signal…
UniProt: J9PAS6, A0A7I9EWR8, Q00004, G1STG2, P61010, A0A5F9CI80, P33731
Ligands: GNP, GTP, MG
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 8 distinct chains · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Srp RNA	rna	165	—	—
q	Signal recognition particle 19	protein	104	28% helix, 19% strand	J9PAS6
s	EM14S01-3B_G0054400.MRNA.1.CDS.1	protein	20	90% helix, 0% strand	A0A7I9EWR8
u	Signal recognition particle subunit SRP68,SIGNAL recognition particle subunit SRP68	protein	441	73% helix, 0% strand	Q00004
v	Signal recognition particle receptor subunit beta	protein	201	33% helix, 19% strand	G1STG2
x	Signal recognition particle 54 kda protein	protein	393	56% helix, 9% strand	P61010
y	Srp receptor subunit alpha	protein	454	48% helix, 16% strand	A0A5F9CI80
z	Signal recognition particle subunit SRP72	protein	62	23% helix, 0% strand	P33731

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains x, y, z
GTP · Guanosine-5'-triphosphate · ligand · chains v
MG · Magnesium ion · metal · 3 copies · chains v, x, y

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	761	0.82	0.85	78	GNP, MG
2	1034	0.75	0.78	85	empty
3	736	0.75	0.81	51	empty
4	1036	0.74	0.77	76	empty
5	445	0.71	0.82	49	empty

Interfaces

13 interfaces between chains.

1–u · 1859 Å² buried · 31 hydrogen bonds · protein-nucleic
v–y · 1797 Å² buried · 22 hydrogen bonds · protein-protein
x–y · 1562 Å² buried · 20 hydrogen bonds · protein-protein
1–z · 1121 Å² buried · 17 hydrogen bonds · protein-nucleic
x–z · 960 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7OBQ · SRP-SR at the distal site conformation · the same entry in another collection · chain z against z, TM-score 1.00
P61010 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein (P61010) · a predicted model of the same protein · chain x against A, TM-score 0.67
Q00004 · AlphaFold monomer V2.0 prediction for signal recognition particle subunit SRP68 (Q00004) · a predicted model of the same protein · chain u against A, TM-score 0.44
P33731 · AlphaFold monomer V2.0 prediction for signal recognition particle subunit SRP72 (P33731) · a predicted model of the same protein · chain z against A, TM-score 0.39

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 J9PAS6
Every structure of UniProt A0A7I9EWR8
Every structure of UniProt Q00004
Every structure of UniProt G1STG2
Every structure of UniProt P61010
Every structure of UniProt A0A5F9CI80
Every structure of UniProt P33731
Elsewhere: RCSB PDB 7OBQ · PDBe 7OBQ · UniProt J9PAS6 · UniProt A0A7I9EWR8 · UniProt Q00004 · UniProt G1STG2 · UniProt P61010 · UniProt A0A5F9CI80 · UniProt P33731

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