Research workbench

Drosophila melanogaster trappiii partial complex: core plus C8 and C11 attached region

Analyse Drosophila melanogaster trappiii partial complex: core plus C8 and C11 attached… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7B6R
Type: protein
Length: 2,173 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FI18195P1; Trafficking protein particle complex subunit 11; Trafficking protein particle…
UniProt: Q9VW22, Q8IRE3, Q9VSY8, Q9VF82, Q9VA95, Q9VLI9, Q9VUZ1, Q7K2Q8, A1Z8I0
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 10 distinct chains · 48% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	FI18195P1	protein	269	77% helix, 0% strand	Q9VW22
B	Trafficking protein particle complex subunit 11	protein	614	56% helix, 4% strand	Q8IRE3
C	Trafficking protein particle complex subunit	protein	165	44% helix, 17% strand	Q9VSY8
D	GEO08327P1	protein	151	33% helix, 11% strand	Q9VF82
E	Trafficking protein particle complex subunit	protein	145	34% helix, 19% strand	Q9VA95
F	Trafficking protein particle complex subunit	protein	219	24% helix, 23% strand	Q9VLI9
G	Probable trafficking protein particle complex subunit 2	protein	139	42% helix, 20% strand	Q9VUZ1
H	Trafficking protein particle complex subunit 5	protein	164	55% helix, 13% strand	Q7K2Q8
I	Trafficking protein particle complex subunit	protein	169	43% helix, 13% strand	Q9VSY8
J	TRAPPC2L	protein	138	36% helix, 28% strand	A1Z8I0

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	420	0.84	0.92	70	empty
2	159	0.83	0.98	29	empty
3	315	0.80	0.90	58	empty
4	182	0.77	0.92	43	empty
5	90	0.74	0.96	17	empty

Interfaces

16 interfaces between chains.

E–F · 1753 Å² buried · 38 hydrogen bonds · protein-protein
H–I · 1244 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1094 Å² buried · 6 hydrogen bonds · protein-protein
D–J · 1045 Å² buried · 14 hydrogen bonds · protein-protein
F–I · 896 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7B6R · Drosophila melanogaster TRAPPIII partial complex: core plus C8 and C11 attached region · the same entry in another collection · chain E against E, TM-score 1.00
Q9VUZ1 · AlphaFold monomer V2.0 prediction for probable trafficking protein particle complex… · a predicted model of the same protein · chain G against A, TM-score 0.90

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 Q9VW22
Every structure of UniProt Q8IRE3
Every structure of UniProt Q9VSY8
Every structure of UniProt Q9VF82
Every structure of UniProt Q9VA95
Every structure of UniProt Q9VLI9
Every structure of UniProt Q9VUZ1
Every structure of UniProt Q7K2Q8
Every structure of UniProt A1Z8I0
Elsewhere: RCSB PDB 7B6R · PDBe 7B6R · UniProt Q9VW22 · UniProt Q8IRE3 · UniProt Q9VSY8 · UniProt Q9VF82 · UniProt Q9VA95 · UniProt Q9VLI9 · UniProt Q9VUZ1 · UniProt Q7K2Q8 · UniProt A1Z8I0

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