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Structure of retromer VPS29-VPS35C subunits complexed with ridl harpin loop (163-176)

Analyse Structure of retromer VPS29-VPS35C subunits complexed with ridl harpin loop… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OSI
Type: protein
Length: 1,940 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein 29; Vacuolar protein sorting-associated…
UniProt: Q9UBQ0, Q96QK1, G8UZ99
Ligands: NA
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 7 distinct chains · 66% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G, J	Vacuolar protein sorting-associated protein 29	protein	182	14% helix, 37% strand	Q9UBQ0
B	Vacuolar protein sorting-associated protein 35	protein	299	77% helix, 1% strand	Q96QK1
C, I	Interaptin	protein	12	0% helix, 17% strand	G8UZ99
E	Vacuolar protein sorting-associated protein 35	protein	302	74% helix, 1% strand	Q96QK1
F	Interaptin	protein	11	0% helix, 0% strand	G8UZ99
H	Vacuolar protein sorting-associated protein 35	protein	283	77% helix, 0% strand	Q96QK1
K	Vacuolar protein sorting-associated protein 35	protein	293	73% helix, 1% strand	Q96QK1

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains E, H, K
EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, D, E, G, H, J, K

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	709	0.82	0.86	98	EDO
2	521	0.73	0.81	66	empty
3	432	0.71	0.82	41	empty
4	356	0.71	0.83	36	empty
5	477	0.71	0.81	46	empty

Interfaces

11 interfaces between chains.

A–B · 1960 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 1773 Å² buried · 9 hydrogen bonds · protein-protein
J–K · 1732 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 1696 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 487 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

Q9UBQ0 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 29… · a predicted model of the same protein · chain A against A, TM-score 0.99
Q96QK1 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 35… · a predicted model of the same protein · chain H 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 Q9UBQ0
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Every structure of UniProt G8UZ99
Elsewhere: RCSB PDB 5OSI · PDBe 5OSI · UniProt Q9UBQ0 · UniProt Q96QK1 · UniProt G8UZ99

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