Research workbench

Monomer of trappii (closed)

Analyse Monomer of trappii (closed) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7E2D
Type: protein
Length: 3,291 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trapp-associated protein TCA17; Trafficking protein particle complex subunit BET3…
UniProt: P32613, P36149, Q99394, Q03630, Q03784, Q03337, P38334, Q03660, Q04183, P32893
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 11 distinct chains · 32% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trapp-associated protein TCA17	protein	144	31% helix, 19% strand	P32613
C	Trafficking protein particle complex subunit BET3	protein	184	41% helix, 13% strand	P36149
B	Trafficking protein particle complex subunit 33	protein	202	50% helix, 12% strand	Q99394
D	Trafficking protein particle complex subunit BET5	protein	151	28% helix, 17% strand	Q03630
E	Trafficking protein particle complex subunit 23	protein	166	31% helix, 15% strand	Q03784
F	Trafficking protein particle complex subunit BET3	protein	182	44% helix, 16% strand	P36149
G	Trafficking protein particle complex subunit 31	protein	204	42% helix, 13% strand	Q03337
H	Trafficking protein particle complex subunit 20	protein	147	35% helix, 21% strand	P38334
I	Trafficking protein particle complex II-specific subunit 130	protein	788	29% helix, 15% strand	Q03660
J	Trafficking protein particle complex II-specific subunit 120	protein	872	29% helix, 13% strand	Q04183
K	Trafficking protein particle complex II-specific subunit 65	protein	251	11% helix, 38% strand	P32893

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	1031	0.83	0.84	130	empty
2	196	0.82	0.95	32	empty
3	214	0.79	0.93	43	empty
4	597	0.78	0.84	82	empty
5	787	0.77	0.82	96	empty

Interfaces

17 interfaces between chains.

G–H · 2399 Å² buried · 38 hydrogen bonds · protein-protein
C–B · 2084 Å² buried · 14 hydrogen bonds · protein-protein
F–G · 1659 Å² buried · 15 hydrogen bonds · protein-protein
J–K · 1416 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 1347 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

7E2D · Monomer of TRAPPII (Closed) · the same entry in another collection · chain K against K, TM-score 1.00
P36149 · AlphaFold monomer V2.0 prediction for trafficking protein particle complex subunit BET3… · a predicted model of the same protein · chain F against A, TM-score 0.95

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 P36149
Every structure of UniProt Q99394
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
Elsewhere: RCSB PDB 7E2D · PDBe 7E2D · UniProt P32613 · UniProt P36149 · UniProt Q99394 · UniProt Q03630 · UniProt Q03784 · UniProt Q03337 · UniProt P38334 · UniProt Q03660 · UniProt Q04183 · UniProt P32893

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