Research workbench

Intact YPT32-trappii (dimer).

Analyse Intact YPT32-trappii (dimer). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EA3
Type: protein
Length: 6,974 residues
Chains: 24
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trapp-associated protein TCA17; Trafficking protein particle complex subunit 33…
UniProt: P32613, Q99394, P36149, Q03630, Q03784, Q03337, P38334, Q03660, Q04183, P32893, P51996
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 12 distinct chains · 29% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, N	Trapp-associated protein TCA17	protein	144	31% helix, 19% strand	P32613
B, O	Trafficking protein particle complex subunit 33	protein	197	45% helix, 13% strand	Q99394
C, P	Trafficking protein particle complex subunit BET3	protein	185	40% helix, 16% strand	P36149
D, Q	Trafficking protein particle complex subunit BET5	protein	151	28% helix, 21% strand	Q03630
E, R	Trafficking protein particle complex subunit 23	protein	162	30% helix, 15% strand	Q03784
F, S	Trafficking protein particle complex subunit BET3	protein	183	43% helix, 16% strand	P36149
G, T	Trafficking protein particle complex subunit 31	protein	202	40% helix, 10% strand	Q03337
H, U	Trafficking protein particle complex subunit 20	protein	147	28% helix, 22% strand	P38334
I, V	Trafficking protein particle complex II-specific subunit 130	protein	788	26% helix, 12% strand	Q03660
J, W	Trafficking protein particle complex II-specific subunit 120	protein	883	26% helix, 16% strand	Q04183
K, X	Trafficking protein particle complex II-specific subunit 65	protein	251	11% helix, 33% strand	P32893
L, Y	GTP-binding protein YPT32/YPT11	protein	194	26% helix, 23% strand	P51996

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	184	0.83	0.96	32	empty
2	282	0.82	0.92	44	empty
3	1073	0.82	0.83	166	empty
4	300	0.81	0.91	49	empty
5	245	0.81	0.92	39	empty

Interfaces

49 interfaces between chains.

G–H · 2385 Å² buried · 34 hydrogen bonds · protein-protein
T–U · 2339 Å² buried · 34 hydrogen bonds · protein-protein
O–P · 2068 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 2068 Å² buried · 22 hydrogen bonds · protein-protein
F–G · 1684 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7EA3 · Intact Ypt32-TRAPPII (dimer). · the same entry in another collection · chain H against H, TM-score 1.00

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 P32613
Every structure of UniProt Q99394
Every structure of UniProt P36149
Every structure of UniProt Q03630
Every structure of UniProt Q03784
Every structure of UniProt Q03337
Every structure of UniProt P38334
Every structure of UniProt Q03660
Every structure of UniProt Q04183
Every structure of UniProt P32893
Every structure of UniProt P51996
Elsewhere: RCSB PDB 7EA3 · PDBe 7EA3 · UniProt P32613 · UniProt Q99394 · UniProt P36149 · UniProt Q03630 · UniProt Q03784 · UniProt Q03337 · UniProt P38334 · UniProt Q03660 · UniProt Q04183 · UniProt P32893 · UniProt P51996

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