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Structure of retromer VPS29-VPS35C subunits complexed with ridl N- terminal domain (1-236)

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

PDB: 5OSH
Type: protein
Length: 2,767 residues
Chains: 12
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
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 9 distinct chains · 59% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G, J	Vacuolar protein sorting-associated protein 29	protein	182	15% helix, 37% strand	Q9UBQ0
B	Vacuolar protein sorting-associated protein 35	protein	299	74% helix, 0% strand	Q96QK1
C	Interaptin	protein	217	53% helix, 3% strand	G8UZ99
E	Vacuolar protein sorting-associated protein 35	protein	294	71% helix, 1% strand	Q96QK1
F	Interaptin	protein	214	55% helix, 3% strand	G8UZ99
H	Vacuolar protein sorting-associated protein 35	protein	290	73% helix, 1% strand	Q96QK1
I	Interaptin	protein	223	51% helix, 2% strand	G8UZ99
K	Vacuolar protein sorting-associated protein 35	protein	293	66% helix, 0% strand	Q96QK1
L	Interaptin	protein	209	52% helix, 2% strand	G8UZ99

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	423	0.78	0.86	63	empty
2	79	0.77	0.98	17	empty
3	155	0.76	0.93	27	empty
4	360	0.74	0.85	47	empty
5	347	0.70	0.83	39	empty

Interfaces

15 interfaces between chains.

D–E · 1770 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1766 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 1657 Å² buried · 8 hydrogen bonds · protein-protein
J–K · 1628 Å² buried · 10 hydrogen bonds · protein-protein
B–H · 884 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5OSH · Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236) · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

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Every structure of UniProt Q9UBQ0
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Elsewhere: RCSB PDB 5OSH · PDBe 5OSH · UniProt Q9UBQ0 · UniProt Q96QK1 · UniProt G8UZ99

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