MolNFT v1 · #157742 · protein

Structure of unliganded HSP90-beta N-terminal domain

6N8W · Heat shock protein HSP 90-beta: “Structure of unliganded HSP90-beta N-terminal domain”. X-ray diffraction, 8 pockets (best druggability 0.64). MolNFT v1 #157742 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6N8W
Type: protein
Length: 883 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein HSP 90-beta
UniProt: P08238
Pockets: 8 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Heat shock protein HSP 90-beta	protein	219	39% helix, 25% strand	P08238
B	Heat shock protein HSP 90-beta	protein	220	35% helix, 21% strand	P08238
C	Heat shock protein HSP 90-beta	protein	225	37% helix, 20% strand	P08238

Ligands and binding sites

GOL · Glycerol · additive · 33 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	322	0.64	0.79	28	GOL
2	496	0.64	0.76	58	GOL
3	208	0.64	0.83	27	GOL
4	279	0.61	0.79	36	GOL
5	231	0.60	0.80	26	GOL

Interfaces

5 interfaces between chains.

A–C · 753 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 665 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 622 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 590 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 531 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6N8W · Structure of Unliganded Hsp90-Beta N-Terminal Domain · the same entry in another collection · chain B against B, TM-score 1.00
P08238 · AlphaFold monomer V2.0 prediction for heat shock protein HSP 90-beta (P08238) · a predicted model of the same protein · chain B against A, TM-score 0.78

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 P08238
Elsewhere: RCSB PDB 6N8W · PDBe 6N8W · UniProt P08238

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