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Structure of TRAP1 complexed with DN401

Analyse Structure of TRAP1 complexed with DN401 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y3N
Type: protein
Length: 438 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein 75 kda, mitochondrial
UniProt: Q12931
Ligands: 8MF
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock protein 75 kda, mitochondrial	protein	438	36% helix, 23% strand	Q12931

Ligands and binding sites

8MF · 1-[(6-bromanyl-1,3-benzodioxol-5-yl)methyl]-4-chloranyl-pyrazolo[3,4-d]pyrimidin-6-amine · ligand · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.67	0.85	30	8MF
2	344	0.60	0.77	36	empty
3	93	0.46	0.80	19	empty
4	87	0.37	0.76	15	empty
5	59	0.31	0.76	19	empty

Compared structures

5Y3N · Structure of TRAP1 complexed with DN401 · the same entry in another collection · chain A against A, TM-score 1.00
Q12931 · AlphaFold monomer V2.0 prediction for heat shock protein 75 kda, mitochondrial (Q12931) · a predicted model of the same protein · chain A against A, TM-score 0.85

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 Q12931
Elsewhere: RCSB PDB 5Y3N · PDBe 5Y3N · UniProt Q12931

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