MolNFT v1 · #138714 · protein

Structure of human apo-SRP72

5WRW · Signal recognition particle subunit SRP72: “Structure of human apo-SRP72”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.49). MolNFT v1 #138714 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5WRW
Type: protein
Length: 780 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Signal recognition particle subunit SRP72
UniProt: O76094
Ligands: SO4
Pockets: 5 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Signal recognition particle subunit SRP72	protein	130	72% helix, 0% strand	O76094

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains C, F

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	200	0.49	0.75	31	empty
2	170	0.47	0.76	24	empty
3	161	0.45	0.75	33	empty
4	94	0.38	0.76	16	empty
5	63	0.31	0.76	14	empty

Interfaces

5 interfaces between chains.

A–B · 620 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 604 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 525 Å² buried · 1 hydrogen bond · protein-protein
B–C · 474 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 455 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5WRW · Structure of human apo-SRP72 · the same entry in another collection · chain C against C, TM-score 1.00
O76094 · AlphaFold monomer V2.0 prediction for signal recognition particle subunit SRP72 (O76094) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O76094
Elsewhere: RCSB PDB 5WRW · PDBe 5WRW · UniProt O76094

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