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Crystal structure of a trapp subassembly activating the rab YPT1P

Analyse Crystal structure of a trapp subassembly activating the rab YPT1P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CUE
Type: protein
Length: 4,036 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transport protein particle 23 kda subunit; Transport protein particle 31 kda subunit…
UniProt: Q03784, Q03337, Q03630, P36149, P01123
Ligands: PLM
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 42% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, M, S	Transport protein particle 23 kda subunit	protein	159	35% helix, 18% strand	Q03784
B, H, N, T	Transport protein particle 31 kda subunit	protein	167	49% helix, 11% strand	Q03337
C, I, O, U	Transport protein particle 18 kda subunit	protein	143	34% helix, 16% strand	Q03630
D, J, P, V	Transport protein particle 22 kda subunit	protein	186	46% helix, 8% strand	P36149
E, K, Q, W	Transport protein particle 22 kda subunit	protein	188	49% helix, 10% strand	P36149
F, L, R, X	GTP-binding protein YPT1	protein	166	34% helix, 19% strand	P01123

Ligands and binding sites

PLM · Palmitic acid · ligand · 4 copies · chains E, K, Q, W

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

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	1104	0.81	0.82	111	PLM
2	657	0.81	0.85	83	PLM
3	302	0.81	0.91	56	empty
4	121	0.80	0.98	23	empty
5	120	0.80	0.97	20	empty

Interfaces

46 interfaces between chains.

B–D · 1588 Å² buried · 15 hydrogen bonds · protein-protein
N–P · 1585 Å² buried · 14 hydrogen bonds · protein-protein
T–V · 1583 Å² buried · 14 hydrogen bonds · protein-protein
H–J · 1582 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1519 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 lipid (palmitoylation).

Compared structures

3CUE · Crystal structure of a TRAPP subassembly activating the Rab Ypt1p · the same entry in another collection · chain J against J, 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 Q03784
Every structure of UniProt Q03337
Every structure of UniProt Q03630
Every structure of UniProt P36149
Every structure of UniProt P01123
Elsewhere: RCSB PDB 3CUE · PDBe 3CUE · UniProt Q03784 · UniProt Q03337 · UniProt Q03630 · UniProt P36149 · UniProt P01123

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