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HSP72-nbd bound to compound tci 8 - TYR15 in down-conformation

Analyse HSP72-nbd bound to compound tci 8 - TYR15 in down-conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MKS
Type: protein
Length: 381 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock 70 kda protein 1A
UniProt: P0DMV8
Ligands: TI8
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock 70 kda protein 1A	protein	381	41% helix, 28% strand	P0DMV8

Ligands and binding sites

TI8 · 3-[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[(4-chlorophenyl)methylamino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propyl prop-2-enoate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	549	0.67	0.77	58	TI8
2	69	0.41	0.80	21	empty

Compared structures

5MKS · HSP72-NBD bound to compound TCI 8 - Tyr15 in down-conformation · the same entry in another collection · chain A against A, TM-score 1.00
P0DMV8 · AlphaFold monomer V2.0 prediction for heat shock 70 kda protein 1A (P0DMV8) · 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 P0DMV8
Elsewhere: RCSB PDB 5MKS · PDBe 5MKS · UniProt P0DMV8

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